2GSV

X-Ray Crystal Structure of Protein YvfG from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR478.

PDB DOI: https://doi.org/10.2210/pdb2GSV/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-04-26 Released: 2006-05-09
Deposition Author(s): Forouhar, F., Su, M., Jayaraman, S., Wang, D., Fang, Y., Cunningham, K., Conover, K., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.264 (Depositor), 0.255 (DCC)
R-Value Work:
0.229 (Depositor), 0.218 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Hypothetical Protein YvfG from Bacillus subtilis, Northeast Structural Genomics Target SR478

Forouhar, F., Su, M., Jayaraman, S., Wang, D., Fang, Y., Cunningham, K., Conover, K., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 19.59 kDa
Atom Count: 1,203
Modelled Residue Count: 135
Deposited Residue Count: 160
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yvfG	A, B	80	Bacillus subtilis	Mutation(s): 3 Gene Names: yvfG
UniProt
Find proteins for P71066 (Bacillus subtilis (strain 168)) Explore P71066 Go to UniProtKB: P71066
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P71066
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.264 (Depositor), 0.255 (DCC)
R-Value Work: 0.229 (Depositor), 0.218 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.048	α = 90
b = 31.645	β = 94.63
c = 53.357	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-05-09
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary