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Found 1 Document (0.824 seconds)

BMRB: 15568

2JXP

Solution NMR Structure of uncharacterized Lipoprotein B from Nitrosomona europaea. Northeast Structural Genomics Target NeR45A.

Authors

Rossi, P., Wang, D., Janjua, H., Owens, L., Xiao, R., Baran, M.C., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T.

Assembly

NeR45A

Entity

1. NeR45A (polymer, Thiol state: not present), 155 monomers, 17583.99 Da Detail

MGFKLRGQVS ELPFERVYIT APAGLTIGSD LERVISTHTR AKVVNKAEKS EAIIQIVHAI REKRILSLSE SGRVREFELV YRVAARLLDA HNAELASLQE IRLTRILPFL DAQELAKAAE EEMLYKDMQK DAVQQILRQV SAFTSAGLEH HHHHH

Formula weight

17583.99 Da

Source organism

Nitrosomonas europaea

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 91.2 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.2 % (1664 of 1825)	89.7 % (850 of 948)	92.0 % (658 of 715)	96.3 % (156 of 162)
Backbone	95.6 % (883 of 924)	94.9 % (297 of 313)	95.9 % (440 of 459)	96.1 % (146 of 152)
Sidechain	87.8 % (922 of 1050)	87.1 % (553 of 635)	88.6 % (359 of 405)	100.0 % (10 of 10)
Aromatic	62.7 % (69 of 110)	65.5 % (36 of 55)	60.0 % (33 of 55)
Methyl	99.0 % (206 of 208)	98.1 % (102 of 104)	100.0 % (104 of 104)

1. NeR45A

MGFKLRGQVS ELPFERVYIT APAGLTIGSD LERVISTHTR AKVVNKAEKS EAIIQIVHAI REKRILSLSE SGRVREFELV YRVAARLLDA HNAELASLQE IRLTRILPFL DAQELAKAAE EEMLYKDMQK DAVQQILRQV SAFTSAGLEH HHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.010 U-[15N-13C]

#	Name	Isotope labeling	Concentration
9	entity	natural abundance	0.86 mM
10	MES	natural abundance	20 mM
11	calcium chloride	natural abundance	5 mM
12	DTT	natural abundance	100 mM
13	sodium chloride	natural abundance	100 mM
14	sodium azide	natural abundance	0.02 %
15	D2O	[U-100% 2H]	100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.008 U-15N, 5%13C

#	Name	Isotope labeling	Concentration
16	entity	natural abundance	1.3 mM
17	MES	natural abundance	20 mM
18	calcium chloride	natural abundance	5 mM
19	DTT	natural abundance	100 mM
20	sodium chloride	natural abundance	100 mM
21	sodium azide	natural abundance	0.02 %
22	D2O	[U-100% 2H]	5 %
23	H2O		95 %

LACS Plot; CA

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

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.09 ppm, Outliers: 4 Detail

LACS Plot; CO

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

Referencing offset: 0.05 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2007-12-10

Citation

Solution NMR Structure of Uncharacterized Lipoprotein B from Nitrosomona europaea. Northeast Structural Genomics Target NeR45A
Rossi, P., Xiao, R., Acton, T.B., Montelione, G.T.

Related entities 1. NeR45A, : 1 : 8 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

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

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

4 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

5 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

8 3D SIMULTANEOUS 15N-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.010 U-[15N-13C]

#	Name	Isotope labeling	Concentration
9	entity	natural abundance	0.86 mM
10	MES	natural abundance	20 mM
11	calcium chloride	natural abundance	5 mM
12	DTT	natural abundance	100 mM
13	sodium chloride	natural abundance	100 mM
14	sodium azide	natural abundance	0.02 %
15	D2O	[U-100% 2H]	100 %

10 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

12 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

13 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.008 U-15N, 5%13C

#	Name	Isotope labeling	Concentration
16	entity	natural abundance	1.3 mM
17	MES	natural abundance	20 mM
18	calcium chloride	natural abundance	5 mM
19	DTT	natural abundance	100 mM
20	sodium chloride	natural abundance	100 mM
21	sodium azide	natural abundance	0.02 %
22	D2O	[U-100% 2H]	5 %
23	H2O		95 %

14 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

15 3D HNCACO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

16 2D 1H-13C HSQC (arom)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NeR45A.009 U-[15N-13C]

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1 mM
2	MES	natural abundance	20 mM
3	calcium chloride	natural abundance	5 mM
4	DTT	natural abundance	100 mM
5	sodium chloride	natural abundance	100 mM
6	sodium azide	natural abundance	0.02 %
7	D2O	[U-100% 2H]	5 %
8	H2O		95 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15568_2jxp.nef
Input source #2: Coordindates	2jxp.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
MGFKLRGQVSELPFERVYITAPAGLTIGSDLERVISTHTRAKVVNKAEKSEAIIQIVHAIREKRILSLSESGRVREFELVYRVAARLLDAHNAELASLQE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGFKLRGQVSELPFERVYITAPAGLTIGSDLERVISTHTRAKVVNKAEKSEAIIQIVHAIREKRILSLSESGRVREFELVYRVAARLLDAHNAELASLQE

-------110-------120-------130-------140-------150-----
IRLTRILPFLDAQELAKAAEEEMLYKDMQKDAVQQILRQVSAFTSAGLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
IRLTRILPFLDAQELAKAAEEEMLYKDMQKDAVQQILRQVSAFTSAGLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	155	0	0	100.0

Content subtype: combined_15568_2jxp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1649		96.1 (chain: A, length: 155)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2802 (1)	noe	94.8 (chain: A, length: 155)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 96.1%
- Total number of assignments
  - ¹H chemical shifts: 846
  - ¹³C chemical shifts: 650
  - ¹⁵N chemical shifts: 153
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	948	846	89.2
¹³C chemical shifts	715	650	90.9
¹⁵N chemical shifts	175	153	87.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	313	297	94.9
¹³C chemical shifts	310	295	95.2
¹⁵N chemical shifts	152	143	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	635	549	86.5
¹³C chemical shifts	405	355	87.7
¹⁵N chemical shifts	23	10	43.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	105	98.1
¹³C chemical shifts	107	105	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	31	56.4
¹³C chemical shifts	55	31	56.4

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 94.8%
- Total number of restraints: 2800
- Weight of restraints: 1.0 (2800)
- Potential type of restraints: square-well-parabolic (2800)
- Range of distance target values: 2.37, 4.2 (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 Lipoprotein B, NMR Structure

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Found 1 Document (0.824 seconds)

BMRB: 15568

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NeR45A, : 1 : 8 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 3 contents Detail