BMRB Entry 16384

Name: Solution NMR Structure of protein yutD from B.subtilis, Northeast Structural Genomics Consortium Target Target SR232
Published: 2009-07-07

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PDB ID: 2kl5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16384
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR Structure of protein yutD from B.subtilis, Northeast Structural Genomics Consortium Target Target SR232

Deposition date:

2009-06-30

Original release date:

2009-07-07

Authors:

Liu, G.; Hamilton, H.; Xiao, R.; Ciccosanti, C.; Ho, K.; Everett, J.; Nair, R.; Acton, T.; Rost, B.; Montelione, G.

Citation:

Citation: Liu, G.; Hamilton, H.; Xiao, R.; Ciccosanti, C.; Ho, K.; Everett, J.; Nair, R.; Acton, T.; Rost, B.; Montelione, G.. "Solution NMR Structure of protein yutD from B.subtilis, Northeast Structural Genomics Consortium Target Target SR232" To be published ., .-..

Assembly members:

Assembly members:
SR232, polymer, 110 residues, 13241.087 Da.

Natural source:

Natural source: Common Name: Bacillus subtilis Taxonomy ID: 1423 Superkingdom: Bacteria Kingdom: not available Genus/species: Bacillus subtilis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: BL21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SR232: MIGMSEKRGEIMILIQNAEF ELVHNFKDGFNEEAFKARYS DILNKYDYIVGDWGYGQLRL KGFFDDQNQKATFETKISTL DEYIYEYCNFGCAYFVLKRI RKLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	382
15N chemical shifts	72
1H chemical shifts	623

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SR232	1

Entities:

Entity 1, SR232 110 residues - 13241.087 Da.

1	MET	ILE	GLY	MET	SER	GLU	LYS	ARG	GLY	GLU
2	ILE	MET	ILE	LEU	ILE	GLN	ASN	ALA	GLU	PHE
3	GLU	LEU	VAL	HIS	ASN	PHE	LYS	ASP	GLY	PHE
4	ASN	GLU	GLU	ALA	PHE	LYS	ALA	ARG	TYR	SER
5	ASP	ILE	LEU	ASN	LYS	TYR	ASP	TYR	ILE	VAL
6	GLY	ASP	TRP	GLY	TYR	GLY	GLN	LEU	ARG	LEU
7	LYS	GLY	PHE	PHE	ASP	ASP	GLN	ASN	GLN	LYS
8	ALA	THR	PHE	GLU	THR	LYS	ILE	SER	THR	LEU
9	ASP	GLU	TYR	ILE	TYR	GLU	TYR	CYS	ASN	PHE
10	GLY	CYS	ALA	TYR	PHE	VAL	LEU	LYS	ARG	ILE
11	ARG	LYS	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

Samples:

sample_1: SR232, [U-100% 13C; U-100% 15N], 1.1 mM; DTT 10 mM; Arginine 50 mM; Bis-Tris pH 6.5 50 mM; DSS 50 uM; NaN3 0.02%; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-13C arom NOESY	sample_1	isotropic	sample_conditions_1
3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - geometry optimization, refinement, structure solution

AutoStruct v2.1, Huang, Tejero, Powers and Montelione - data analysis, refinement

AutoAssign v2.1, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment, data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

TOPSPIN, Bruker Biospin - collection

VNMRJ, Varian - collection

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization, refinement, structure solution

NMR spectrometers:

Bruker Avance 800 MHz
Varian INOVA 600 MHz

PDB	2KL5
DBJ	BAI86771 BAM55300 BAM59313 GAK81980
EMBL	CAB15221 CCU60272 CEI58480 CEJ78885 CJS52863
GB	ADM39188 ADV94035 AEP88101 AEP92247 AFI29777
REF	NP_391111 WP_003222892 WP_003228682 WP_010329969 WP_017696728
SP	O32127
AlphaFold	O32127

1	MET	ILE	GLY	MET	SER	GLU	LYS	ARG	GLY	GLU
2	ILE	MET	ILE	LEU	ILE	GLN	ASN	ALA	GLU	PHE
3	GLU	LEU	VAL	HIS	ASN	PHE	LYS	ASP	GLY	PHE
4	ASN	GLU	GLU	ALA	PHE	LYS	ALA	ARG	TYR	SER
5	ASP	ILE	LEU	ASN	LYS	TYR	ASP	TYR	ILE	VAL
6	GLY	ASP	TRP	GLY	TYR	GLY	GLN	LEU	ARG	LEU
7	LYS	GLY	PHE	PHE	ASP	ASP	GLN	ASN	GLN	LYS
8	ALA	THR	PHE	GLU	THR	LYS	ILE	SER	THR	LEU
9	ASP	GLU	TYR	ILE	TYR	GLU	TYR	CYS	ASN	PHE
10	GLY	CYS	ALA	TYR	PHE	VAL	LEU	LYS	ARG	ILE
11	ARG	LYS	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

1	MET	ILE	GLY	MET	SER	GLU	LYS	ARG	GLY	GLU
2	ILE	MET	ILE	LEU	ILE	GLN	ASN	ALA	GLU	PHE
3	GLU	LEU	VAL	HIS	ASN	PHE	LYS	ASP	GLY	PHE
4	ASN	GLU	GLU	ALA	PHE	LYS	ALA	ARG	TYR	SER
5	ASP	ILE	LEU	ASN	LYS	TYR	ASP	TYR	ILE	VAL
6	GLY	ASP	TRP	GLY	TYR	GLY	GLN	LEU	ARG	LEU
7	LYS	GLY	PHE	PHE	ASP	ASP	GLN	ASN	GLN	LYS
8	ALA	THR	PHE	GLU	THR	LYS	ILE	SER	THR	LEU
9	ASP	GLU	TYR	ILE	TYR	GLU	TYR	CYS	ASN	PHE
10	GLY	CYS	ALA	TYR	PHE	VAL	LEU	LYS	ARG	ILE
11	ARG	LYS	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS