3U3X | pdb_00003u3x

Crystal structure of a putative oxidoreductase from Sinorhizobium meliloti 1021

PDB DOI: https://doi.org/10.2210/pdb3U3X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-10-06 Released: 2011-10-19
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: 2.79 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (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 a putative oxidoreductase from Sinorhizobium meliloti 1021

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

To be published.

Macromolecule Content

Total Structure Weight: 200.94 kDa
Atom Count: 12,240
Modeled Residue Count: 1,650
Deposited Residue Count: 1,805
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B [auth D], C [auth G], D [auth J], E [auth M]	361	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: R00114, SMc04138 EC: 1
UniProt
Find proteins for Q92T66 (Rhizobium meliloti (strain 1021)) Explore Q92T66 Go to UniProtKB: Q92T66
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92T66
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G MOL2 format, chain F [auth A] MOL2 format, chain G mmCIF format, chain F [auth A] mmCIF format, chain G	F [auth A], G	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G Interactions & Density Focus chain F [auth A] Focus chain G

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 257.055	α = 90
b = 71.028	β = 104.68
c = 129.002	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-10-19

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-10-19
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: 2024-10-30
Changes: Structure summary