3QVO

Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.

PDB DOI: https://doi.org/10.2210/pdb3QVO/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Shigella flexneri 2a str. 2457T
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-02-25 Released: 2011-06-01
Deposition Author(s): Cuff, M.E., Xu, X., Cui, H., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.251
R-Value Work: 0.215
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.

Cuff, M.E., Xu, X., Cui, H., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 26.62 kDa
Atom Count: 1,607
Modelled Residue Count: 197
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NmrA family protein	A	236	Shigella flexneri 2a str. 2457T	Mutation(s): 0 Gene Names: S1416, SF2457T_2192
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MNB Query on MNB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5-MERCAPTO-2-NITRO-BENZOIC ACID C₇ H₅ N O₄ S GANZODCWZFAEGN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.251
R-Value Work: 0.215
R-Value Observed: 0.217
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.524	α = 90
b = 73.524	β = 90
c = 130.246	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-10-03
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.