BMRB Entry 7260

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PDB ID: 2hgc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR7260
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of the YjcQ protein from Bacillus subtilis. Northeast Structural Genomics target SR346. (CASP Target)

Deposition date:

2006-08-10

Original release date:

2007-02-01

Authors:

Rossi, P.; Cort, J.; Ho, C.; Janjua, H.; Cunningham, K.; Ma, L.-C.; Xiao, R.; Liu, J.; Baran, M.; Swapna, G.; Acton, T.; Rost, B.; Kennedy, M.; Montelione, G.

Citation:

Citation: Rossi, P.; Cort, J.; Ho, C.; Janjua, H.; Cunningham, K.; Ma, L.-C.; Xiao, R.; Liu, J.; Baran, M.; Swapna, G.; Acton, T.; Rost, B.; Kennedy, M.; Montelione, G.. "Solution NMR structure of the YjcQ protein from Bacillus subtilis. Northeast Structural Genomics target SR346. (CASP Target)" .

Assembly members:

Assembly members:
YjcQ protein, polymer, 102 residues, Formula weight is not available

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YjcQ protein: MNKDKLRYAILKEIFEGNTP LSENDIGVTEDQFDDAVNFL KREGYIIGVHYSDDRPHLYK LGPELTEKGENYLKENGTWS KAYKTIKEIKDWIKLEHHHH HH

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1

Data type	Count
13C chemical shifts	368
15N chemical shifts	89
1H chemical shifts	567

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YjcQ protein	1

Entities:

Entity 1, YjcQ protein 102 residues - Formula weight is not available

1

MET

ASN

LYS

ASP

LYS

LEU

ARG

TYR

ALA

ILE

2

LEU

LYS

GLU

ILE

PHE

GLU

GLY

ASN

THR

PRO

3

LEU

SER

GLU

ASN

ASP

ILE

GLY

VAL

THR

GLU

4

ASP

GLN

PHE

ASP

ALA

VAL

ASN

PHE

LEU

5

LYS

ARG

GLU

GLY

TYR

ILE

GLY

VAL

HIS

6

TYR

SER

ASP

ARG

PRO

HIS

LEU

TYR

LYS

7

LEU

GLY

PRO

GLU

LEU

THR

GLU

LYS

GLY

GLU

8

ASN

TYR

LEU

LYS

GLU

ASN

GLY

THR

TRP

SER

9

LYS

ALA

TYR

LYS

THR

ILE

LYS

GLU

ILE

LYS

10

ASP

TRP

ILE

LYS

LEU

GLU

HIS

11

HIS

Samples:

sample_1: YjcQ protein, [U-13C; U-15N], 0.85 mM; CaCl2 5 mM; NaCl 100 mM; NH4OAc 20 mM; DTT 10 mM; NaN3 0.02%; D2O 5%; H2O 95%

sample_2: YjcQ protein, [U-5% 13C; U-15N], 0.77 mM; CaCl2 5 mM; NaCl 100 mM; NH4OAc 20 mM; DTT 10 mM; NaN3 0.02%; D2O 5%; H2O 95%

sample_cond_1: ionic strength: 0.1 M; pH: 5.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	not available	not available	not available
3D 15N-separated NOESY	not available	not available	not available
HcCH-TOCSY	not available	not available	not available
HcCH-COSY	not available	not available	not available
CccoNH-TOCSY	not available	not available	not available
3D-HNCACB	not available	not available	not available
HNcoCACB	not available	not available	not available
HBHAcoNH	not available	not available	not available
HNCO	not available	not available	not available
13C HSQC noct Stereospecific VL Me assign.	not available	not available	not available
Het-NOE	not available	not available	not available
T1/T1rho	not available	not available	not available

Software:

VNMR v6.1C - collection

xwinnmr v3.5 - collection

DYANA v1.2 - structure solution

X-PLOR v2.11.2 - refinement

NMRPipe v2005 - processing

SPARKY v3.11 - data analysis

AutoAssign v2.2.1 - data analysis

AutoStruct v2.1.1 - structure solution

HYPER v2.1 - structure solution

PDBStat v4.1 - data analysis

PSVS v1.3 - refinement

Procheck NMR v3.51 - refinement

MolProbity v3.01 - refinement

NMR spectrometers:

Varian INOVA 750 MHz

PDB	2HGC
DBJ	BAM50120 BAM57388
EMBL	CAB13052 CEI56338 CEJ76761
GB	AFQ57114 AGG60550 AHA77184 AIC39588 AIC43820
REF	NP_389077 WP_003245536 WP_014906298 WP_024572461 WP_026699368
SP	O31639
AlphaFold	O31639