3UN1 | pdb_00003un1

Crystal structure of an oxidoreductase from Sinorhizobium meliloti 1021

PDB DOI: https://doi.org/10.2210/pdb3UN1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-15 Released: 2011-11-30
Deposition Author(s): Agarwal, R., 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: 2.45 Å
R-Value Free:
0.241 (Depositor), 0.237 (DCC)
R-Value Work:
0.185 (Depositor), 0.182 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of an oxidoreductase from Sinorhizobium meliloti 1021

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 114.52 kDa
Atom Count: 7,202
Modeled Residue Count: 946
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable oxidoreductase	A, B, C, D	260	Sinorhizobium meliloti	Mutation(s): 0 Gene Names: y20210, RB0203, SM_b20210 EC: 1.1.1.100
UniProt
Find proteins for Q7ANT0 (Rhizobium meliloti (strain 1021)) Explore Q7ANT0 Go to UniProtKB: Q7ANT0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7ANT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth C] MOL2 format, chain F [auth D] MOL2 format, chain E [auth C] mmCIF format, chain F [auth D] mmCIF format, chain E [auth C]	E [auth C], F [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.241 (Depositor), 0.237 (DCC)
R-Value Work: 0.185 (Depositor), 0.182 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.225	α = 90
b = 84.225	β = 90
c = 249.238	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-30

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-11-30
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: 2024-11-20
Changes: Structure summary