3RH7 | pdb_00003rh7

Crystal structure of a putative oxidoreductase (SMa0793) from Sinorhizobium meliloti 1021 at 3.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3RH7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-11 Released: 2011-06-08
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.227 (Depositor), 0.240 (DCC)
R-Value Work:
0.187 (Depositor), 0.200 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical oxidoreductase (SMa0793) from SINORHIZOBIUM MELILOTI 1021 at 3.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 207.41 kDa
Atom Count: 12,892
Modeled Residue Count: 1,727
Deposited Residue Count: 1,926
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 oxidoreductase	A, B, C, D, E A, B, C, D, E, F	321	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: RA0429, SMa0793 EC: 1.5.1
UniProt
Find proteins for Q92ZM6 (Rhizobium meliloti (strain 1021)) Explore Q92ZM6 Go to UniProtKB: Q92ZM6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92ZM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain J [auth F] SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth F] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth A] mmCIF format, chain J [auth F] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth A]	G [auth A], H [auth C], I [auth D], J [auth F]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.227 (Depositor), 0.240 (DCC)
R-Value Work: 0.187 (Depositor), 0.200 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33RH7

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.92	α = 90
b = 99.735	β = 90
c = 234.302	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2011-11-16
Changes: Structure summary
Version 1.4: 2014-12-24
Changes: Structure summary
Version 1.5: 2017-11-08
Changes: Refinement description
Version 1.6: 2023-02-01
Changes: Database references, Derived calculations
Version 1.7: 2024-11-06
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.