3UMA | pdb_00003uma

Crystal structure of a hypothetical peroxiredoxin protein frm Sinorhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb3UMA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-11-12 Released: 2011-11-23
Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.213 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a hypothetical peroxiredoxin protein from Sinorhizobium meliloti

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 60.34 kDa
Atom Count: 3,754
Modeled Residue Count: 495
Deposited Residue Count: 552
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 peroxiredoxin protein	A, B, C	184	Sinorhizobium meliloti	Mutation(s): 0 Gene Names: R00915, SMc00072 EC: 1.11.1.27
UniProt
Find proteins for Q92RF9 (Rhizobium meliloti (strain 1021)) Explore Q92RF9 Go to UniProtKB: Q92RF9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92RF9
Sequence Annotations Expand
Reference Sequence

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 D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.241 (Depositor), 0.240 (DCC)
R-Value Work: 0.213 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.063	α = 90
b = 113.063	β = 90
c = 98.823	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-11-23
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-09
Changes: Structure summary