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BMRB: 15652

2K0M

Solution NMR structure of the uncharacterized protein from Rhodospirillum rubrum gene locus Rru_A0810. Northeast Structural Genomics Target RrR43.

Authors

Rossi, P., Wang, H., Jiang, M., Foote, E.L., Xiao, R., Liu, J., Swapna, G., Acton, T.B., Baran, M.C., Rost, B., Montelione, G.T.

Assembly

RrR43

Entity

1. RrR43 (polymer, Thiol state: all free), 104 monomers, 11847.37 Da Detail

MAKAQPIEIA GHEFARKADA LAFMKVMLNR YRPGDIVSTV DGAFLVEALK RHPDATSKIG PGVRNFEVRS ADYGTQCFWI LRTDGSEERF SYKKCVLEHH HHHH

Formula weight

11847.37 Da

Source organism

Rhodospirillum rubrum

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 93.3 %, Completeness: 90.6 %, Completeness (bb): 90.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (1101 of 1215)	90.8 % (573 of 631)	91.0 % (436 of 479)	87.6 % (92 of 105)
Backbone	90.3 % (556 of 616)	91.0 % (192 of 211)	90.8 % (277 of 305)	87.0 % (87 of 100)
Sidechain	91.2 % (635 of 696)	90.7 % (381 of 420)	91.9 % (249 of 271)	100.0 % (5 of 5)
Aromatic	79.7 % (102 of 128)	79.7 % (51 of 64)	79.4 % (50 of 63)	100.0 % (1 of 1)
Methyl	100.0 % (102 of 102)	100.0 % (51 of 51)	100.0 % (51 of 51)

1. RrR43

MAKAQPIEIA GHEFARKADA LAFMKVMLNR YRPGDIVSTV DGAFLVEALK RHPDATSKIG PGVRNFEVRS ADYGTQCFWI LRTDGSEERF SYKKCVLEHH HHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.002

#	Name	Isotope labeling	Concentration
8	RrR43	[U-100% 13C; U-100% 15N]	1.05 mM
9	MES	natural abundance	20 mM
10	DTT	natural abundance	10 mM
11	sodium azide	natural abundance	0.02 %
12	sodium chloride	natural abundance	100 mM
13	DSS	natural abundance	50 uM
14	calcium chloride	natural abundance	5 mM

LACS Plot; CA

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

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.09 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K0M, Strand ID: A Detail

Release date

2008-02-06

Citation

Solution NMR structure of the uncharacterized protein from Rhodospirillum rubrum gene locus Rru_A0810. Northeast Structural Genomics Target RrR43
Rossi, P., Xiao, R., Acton, T.B., Montelione, G.T.

Related entities 1. RrR43, : 1 : 8 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

2 2D 1H-13C HSQC (aliph)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

7 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

9 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

10 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

12 3D 1H-13C NOESY (aliph)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

13 2D 1H-13C HSQC (stereomethyl)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.002

#	Name	Isotope labeling	Concentration
8	RrR43	[U-100% 13C; U-100% 15N]	1.05 mM
9	MES	natural abundance	20 mM
10	DTT	natural abundance	10 mM
11	sodium azide	natural abundance	0.02 %
12	sodium chloride	natural abundance	100 mM
13	DSS	natural abundance	50 uM
14	calcium chloride	natural abundance	5 mM

14 2D 1H-13C HSQC (arom)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

15 3D 1H-13C NOESY (arom)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details RrR43.004

#	Name	Isotope labeling	Concentration
1	RrR43	[U-5% 13C; U-100% 15N]	1.15 mM
2	MES	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM
6	DSS	natural abundance	50 uM
7	calcium chloride	natural abundance	5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15652_2k0m.nef
Input source #2: Coordindates	2k0m.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
MAKAQPIEIAGHEFARKADALAFMKVMLNRYRPGDIVSTVDGAFLVEALKRHPDATSKIGPGVRNFEVRSADYGTQCFWILRTDGSEERFSYKKCVLEHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAKAQPIEIAGHEFARKADALAFMKVMLNRYRPGDIVSTVDGAFLVEALKRHPDATSKIGPGVRNFEVRSADYGTQCFWILRTDGSEERFSYKKCVLEHH

----
HHHH
||||
HHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	0	0	100.0

Content subtype: combined_15652_2k0m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1096		93.3 (chain: A, length: 104)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2237 (1)	noe	92.3 (chain: A, length: 104)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 93.3%
- Total number of assignments
  - ¹H chemical shifts: 571
  - ¹³C chemical shifts: 435
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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	631	571	90.5
¹³C chemical shifts	479	435	90.8
¹⁵N chemical shifts	113	90	79.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	211	190	90.0
¹³C chemical shifts	208	186	89.4
¹⁵N chemical shifts	100	85	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	420	381	90.7
¹³C chemical shifts	271	249	91.9
¹⁵N chemical shifts	13	5	38.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	53	98.1
¹³C chemical shifts	54	53	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	51	79.7
¹³C chemical shifts	63	50	79.4
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 92.3%
- Total number of restraints: 2231
- Weight of restraints: 1.0 (2231)
- Potential type of restraints: square-well-parabolic (2231)
- Range of distance target values: 2.17, 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

Keywords NESG, Solution NMR

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Found 1 Document (0.884 seconds)

BMRB: 15652

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RrR43, : 1 : 8 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 3 contents Detail