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BMRB: 18346

2LR4

NMR structure of the protein NP_390037.1 from Bacillus subtilis.

Authors

Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K., JCSG, J.

Assembly

NP 390037.1 from Bacillus subtilis

Entity

1. NP 390037.1 from Bacillus subtilis (polymer, Thiol state: not present), 128 monomers, 14259.09 Da Detail

GAEALPLYYL QITGITSDGN DFAWDNLTSS QTKAPNVLKG NKLYVKARFM GYTKLTVITG KDGKNLLYNG TAKMFKSDAI LGQNKVVIGW DKYFEIPMDA LQDNSIQIKA LSSGTTFVYS QKIDFERE

Formula weight

14259.09 Da

Source organism

Bacillus subtilis

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 89.5 %, Completeness (bb): 84.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.5 % (1357 of 1517)	96.3 % (756 of 785)	78.2 % (462 of 591)	98.6 % (139 of 141)
Backbone	84.9 % (647 of 762)	95.1 % (251 of 264)	73.2 % (273 of 373)	98.4 % (123 of 125)
Sidechain	94.8 % (827 of 872)	96.9 % (505 of 521)	91.3 % (306 of 335)	100.0 % (16 of 16)
Aromatic	79.3 % (111 of 140)	97.1 % (68 of 70)	60.3 % (41 of 68)	100.0 % (2 of 2)
Methyl	95.9 % (140 of 146)	94.5 % (69 of 73)	97.3 % (71 of 73)

1. entity

GAEALPLYYL QITGITSDGN DFAWDNLTSS QTKAPNVLKG NKLYVKARFM GYTKLTVITG KDGKNLLYNG TAKMFKSDAI LGQNKVVIGW DKYFEIPMDA LQDNSIQIKA LSSGTTFVYS QKIDFERE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LR4, Strand ID: A Detail

Release date

2012-04-29

Citation

NMR structure of the protein NP_390037.1 from Bacillus subtilis
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
Not known

Related entities 1. NP 390037.1 from Bacillus subtilis, : 1 : 1 entities Detail

Experiments performed 7 experiments Detail

1 4D APSY-HACANH

Instrument

Bruker Avance - 600 MHz mbavance601

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

2 5D APSY-HACACONH

Instrument

Bruker Avance - 600 MHz mbavance601

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

3 5D APSY-CBCACONH

Instrument

Bruker Avance - 600 MHz mbavance601

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz mbavance800

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

5 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz mbavance800

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz mbavance800

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz mbavance601

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	NP_390037.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	D2O	[U-99% 2H]		5 %
6	H2O	natural abundance		95 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18346_2lr4.nef
Input source #2: Coordindates	2lr4.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
GAEALPLYYLQITGITSDGNDFAWDNLTSSQTKAPNVLKGNKLYVKARFMGYTKLTVITGKDGKNLLYNGTAKMFKSDAILGQNKVVIGWDKYFEIPMDA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAEALPLYYLQITGITSDGNDFAWDNLTSSQTKAPNVLKGNKLYVKARFMGYTKLTVITGKDGKNLLYNGTAKMFKSDAILGQNKVVIGWDKYFEIPMDA

-------110-------120--------
LQDNSIQIKALSSGTTFVYSQKIDFERE
||||||||||||||||||||||||||||
LQDNSIQIKALSSGTTFVYSQKIDFERE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	128	0	0	100.0

Content subtype: combined_18346_2lr4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1349		99.2 (chain: A, length: 128)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2837 (1)	noe	99.2 (chain: A, length: 128)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 776
  - ¹³C chemical shifts: 432
  - ¹⁵N chemical shifts: 141
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 99.2%
- Total number of restraints: 2837
- Weight of restraints: 1.0 (2837)
- Potential type of restraints: upper-bound-parabolic (2837)
- Range of distance target values: 2.4, 5.5 (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 FAB fragment