3W5S | pdb_00003w5s

Crystal Structure of Maleylacetate Reductase from Rhizobium sp. strain MTP-10005

PDB DOI: https://doi.org/10.2210/pdb3W5S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhizobium sp. MTP-10005
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-02-06 Released: 2014-02-12
Deposition Author(s): Fujii, T., Ogawa, A., Goda, Y., Yamauchi, T., Yoshida, M., Oikawa, T., Hata, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.180 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.168 (DCC)
R-Value Observed:
0.155 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Maleylacetate Reductase from Rhizobium sp. strain MTP-10005

Fujii, T., Ogawa, A., Goda, Y., Yamauchi, T., Yoshida, M., Oikawa, T., Hata, Y.

To be published.

Macromolecule Content

Total Structure Weight: 78.13 kDa
Atom Count: 5,885
Modeled Residue Count: 700
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maleylacetate reductase	A, B	371	Rhizobium sp. MTP-10005	Mutation(s): 0 Gene Names: graC EC: 1.3.1.32
UniProt
Find proteins for A1IIX4 (Rhizobium sp. (strain MTP-10005)) Explore A1IIX4 Go to UniProtKB: A1IIX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1IIX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.180 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.168 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.855	α = 90
b = 121.15	β = 101.48
c = 94.109	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-12
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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