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BMRB: 16560

2KPM

Solution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A

Authors

Rossi, P., Belote, R., Jiang, M., Xiao, R., Ciccosanti, C., Acton, T., Everett, J., Rost, B., Montelione, G.

Assembly

protein from gene locus NE0665

Entity

1. protein from gene locus NE0665 (polymer, Thiol state: not present), 105 monomers, 11919.17 Da Detail

MDQKSSSPQP AAQAPETKQA FPRKFVLAAL EQSSDDAGWA NLGNFGNYLN KLQPDFDSRL YGYKKLSDLV KARTDLFVTE ERQVPGSTQK ALYLRAKLEH HHHHH

Formula weight

11919.17 Da

Source organism

Nitrosomonas europaea

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 89.5 %, Completeness: 84.0 %, Completeness (bb): 86.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.0 % (1046 of 1245)	82.5 % (539 of 653)	85.2 % (409 of 480)	87.5 % (98 of 112)
Backbone	86.7 % (536 of 618)	86.6 % (181 of 209)	86.1 % (267 of 310)	88.9 % (88 of 99)
Sidechain	82.0 % (596 of 727)	80.6 % (358 of 444)	84.4 % (228 of 270)	76.9 % (10 of 13)
Aromatic	79.7 % (94 of 118)	79.7 % (47 of 59)	79.3 % (46 of 58)	100.0 % (1 of 1)
Methyl	97.9 % (92 of 94)	95.7 % (45 of 47)	100.0 % (47 of 47)

1. protein from gene locus NE0665

MDQKSSSPQP AAQAPETKQA FPRKFVLAAL EQSSDDAGWA NLGNFGNYLN KLQPDFDSRL YGYKKLSDLV KARTDLFVTE ERQVPGSTQK ALYLRAKLEH HHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 5%13C,100%15N

#	Name	Isotope labeling	Concentration
10	entity	[U-5% 13C; U-100% 15N]	0.9 mM
11	sodium chloride	natural abundance	200 mM
12	MES	natural abundance	20 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.02 %
15	Calcium Chloride	natural abundance	5 mM
16	DSS	natural abundance	50 uM
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KPM, Strand ID: A Detail

Release date

2010-01-06

Citation

Solution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A
Rossi, P., Xiao, R., Acton, T., Rost, B., Montelione, G.
Not known

Related entities 1. protein from gene locus NE0665, : 1 entities Detail

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

3 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

4 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

5 3D CCH-TOCSY

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

6 3D HNCO

Instrument

Bruker Avance - 800 MHz 5mm cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

7 3D HNCACB

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

9 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz 5mm cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz 5mm cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

12 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

13 3D HNCA

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

14 het-NOE

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 5%13C,100%15N

#	Name	Isotope labeling	Concentration
10	entity	[U-5% 13C; U-100% 15N]	0.9 mM
11	sodium chloride	natural abundance	200 mM
12	MES	natural abundance	20 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.02 %
15	Calcium Chloride	natural abundance	5 mM
16	DSS	natural abundance	50 uM
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

15 T1-pseudo2D

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 5%13C,100%15N

#	Name	Isotope labeling	Concentration
10	entity	[U-5% 13C; U-100% 15N]	0.9 mM
11	sodium chloride	natural abundance	200 mM
12	MES	natural abundance	20 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.02 %
15	Calcium Chloride	natural abundance	5 mM
16	DSS	natural abundance	50 uM
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

16 T2CPMG-pseudo2D

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 5%13C,100%15N

#	Name	Isotope labeling	Concentration
10	entity	[U-5% 13C; U-100% 15N]	0.9 mM
11	sodium chloride	natural abundance	200 mM
12	MES	natural abundance	20 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.02 %
15	Calcium Chloride	natural abundance	5 mM
16	DSS	natural abundance	50 uM
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

17 high-resC13-HSQC

Instrument

Bruker Avance - 800 MHz 5mm cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 5%13C,100%15N

#	Name	Isotope labeling	Concentration
10	entity	[U-5% 13C; U-100% 15N]	0.9 mM
11	sodium chloride	natural abundance	200 mM
12	MES	natural abundance	20 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.02 %
15	Calcium Chloride	natural abundance	5 mM
16	DSS	natural abundance	50 uM
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

18 1D presat referencing

Instrument

Bruker Avance - 600 MHz 1.7 mm Microcryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

19 1D presat referencing

Instrument

Bruker Avance - 800 MHz 5mm cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details U-13C,15N

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.957 mM
2	sodium chloride	natural abundance	200 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	Calcium Chloride	natural abundance	5 mM
7	DSS	natural abundance	50 uM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16560_2kpm.nef
Input source #2: Coordindates	2kpm.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MDQKSSSPQPAAQAPETKQAFPRKFVLAALEQSSDDAGWANLGNFGNYLNKLQPDFDSRLYGYKKLSDLVKARTDLFVTEERQVPGSTQKALYLRAKLEH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDQKSSSPQPAAQAPETKQAFPRKFVLAALEQSSDDAGWANLGNFGNYLNKLQPDFDSRLYGYKKLSDLVKARTDLFVTEERQVPGSTQKALYLRAKLEH

-----
HHHHH
|||||
HHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0

Content subtype: combined_16560_2kpm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1041		87.6 (chain: A, length: 105)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2285 (1)	noe	85.7 (chain: A, length: 105)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	258 (257)	.	84.8 (chain: A, length: 105)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 87.6%
- Total number of assignments
  - ¹H chemical shifts: 538
  - ¹⁵N chemical shifts: 98
  - ¹³C chemical shifts: 405
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	653	538	82.4
¹⁵N chemical shifts	117	98	83.8
¹³C chemical shifts	480	405	84.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	209	181	86.6
¹⁵N chemical shifts	99	87	87.9
¹³C chemical shifts	210	179	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	444	357	80.4
¹⁵N chemical shifts	18	11	61.1
¹³C chemical shifts	270	226	83.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	47	97.9
¹³C chemical shifts	48	47	97.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	47	79.7
¹⁵N chemical shifts	1	1	100.0
¹³C chemical shifts	58	46	79.3

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 85.7%
- Total number of restraints: 2285
- Weight of restraints: 1.0 (2285)
- Potential type of restraints: square-well-parabolic (2285)
- Range of distance target values: 2.25, 4.07 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 84.8%
- Total number of restraints: 257
- Total number of restraints per polymer type: 257
- Weight of restraints: 1.0 (257)
- Potential type of restraints: square-well-parabolic (257)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.559 seconds)

BMRB: 16560

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. protein from gene locus NE0665, : 1 entities Detail

Experiments performed 19 experiments Detail

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NMR combined restraints 4 contents Detail