6LTF | pdb_00006ltf

Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004

PDB DOI: https://doi.org/10.2210/pdb6LTF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Xanthomonas campestris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-01-22 Released: 2021-02-10
Deposition Author(s): Zhu, G.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.212 (Depositor), 0.212 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004

Zhu, G.P.

To be published.

Macromolecule Content

Total Structure Weight: 35.64 kDa
Atom Count: 2,923
Modeled Residue Count: 334
Deposited Residue Count: 335
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase	A	335	Xanthomonas campestris	Mutation(s): 0 Gene Names: D0A35_19175, TR80_00940, XcmpCFBP7700_13825 EC: 1.1.1.41
UniProt
Find proteins for A0A0H2XBX7 (Xanthomonas campestris pv. campestris (strain 8004)) Explore A0A0H2XBX7 Go to UniProtKB: A0A0H2XBX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2XBX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.212 (Depositor), 0.212 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.052	α = 90
b = 156.657	β = 90
c = 68.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-10
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.