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BMRB: 18732

2LYX

NMR structure of the protein NP_390345.1 from Bacilus subtilis

Authors

Proudfoot, A., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

NP 390345.1

Entity

1. NP 390345.1 (polymer, Thiol state: not present), 87 monomers, 10313.75 Da Detail

GEETPLVTAR HMSKWEEIAV KEAKKRYPLA QVLFKQKVWD RKRKDEAVKQ YHLTLREGSK EFGVFVTISF DPYSQKVNKI AILEEYQ

Formula weight

10313.75 Da

Source organism

Bacillus subtilis

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.7 %, Completeness (bb): 83.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.7 % (942 of 1099)	88.8 % (515 of 580)	78.7 % (336 of 427)	98.9 % (91 of 92)
Backbone	83.1 % (429 of 516)	94.8 % (165 of 174)	69.8 % (180 of 258)	100.0 % (84 of 84)
Sidechain	88.9 % (593 of 667)	85.7 % (348 of 406)	94.1 % (238 of 253)	87.5 % (7 of 8)
Aromatic	96.2 % (100 of 104)	96.2 % (50 of 52)	96.0 % (48 of 50)	100.0 % (2 of 2)
Methyl	94.6 % (87 of 92)	93.5 % (43 of 46)	95.7 % (44 of 46)

1. NP 390345.1

GEETPLVTAR HMSKWEEIAV KEAKKRYPLA QVLFKQKVWD RKRKDEAVKQ YHLTLREGSK EFGVFVTISF DPYSQKVNKI AILEEYQ

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 2.19 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 2.19 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 35 models in PDB: 2LYX, Strand ID: A Detail

Release date

2012-10-21

Citation

NMR structure of the protein NP_390345.1 from Bacilus subtilis
Proudfoot, A., Wuthrich, K.
Not known

Related entities 1. NP 390345.1, : 1 : 1 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 APSY 4D-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 APSY 5D-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 APSY 5D-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	NP_390345.1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	calcium chloride	natural abundance		20 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18732_2lyx.nef
Input source #2: Coordindates	2lyx.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-------
GEETPLVTARHMSKWEEIAVKEAKKRYPLAQVLFKQKVWDRKRKDEAVKQYHLTLREGSKEFGVFVTISFDPYSQKVNKIAILEEYQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GEETPLVTARHMSKWEEIAVKEAKKRYPLAQVLFKQKVWDRKRKDEAVKQYHLTLREGSKEFGVFVTISFDPYSQKVNKIAILEEYQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0

Content subtype: combined_18732_2lyx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	941		98.9 (chain: A, length: 87)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1845 (1)	noe	97.7 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 527
  - ¹³C chemical shifts: 324
  - ¹⁵N chemical shifts: 90
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 97.7%
- Total number of restraints: 1825
- Weight of restraints: 1.0 (1825)
- Potential type of restraints: upper-bound-parabolic (1825)
- 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 DUF3889, PF13028