4ZDA | pdb_00004zda

Crystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis

PDB DOI: https://doi.org/10.2210/pdb4ZDA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-17 Released: 2016-06-29
Deposition Author(s): Pojer, F., Murima, P., McKinney, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.257 (Depositor), 0.255 (DCC)
R-Value Work:
0.214 (Depositor), 0.211 (DCC)
R-Value Observed:
0.216 (Depositor)

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Ligand Structure Quality Assessment

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Literature

crystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis

Pojer, F., Murima, P., McKinney, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 514.97 kDa
Atom Count: 34,561
Modeled Residue Count: 4,410
Deposited Residue Count: 4,602
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase (NADP) Icd2	A, B, C, D, E A, B, C, D, E, F	767	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: icd2, MSMEG_1654, MSMEI_1615 EC: 1.1.1.42
UniProt
Find proteins for A0QSZ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSZ3 Go to UniProtKB: A0QSZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QSZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICT Query on ICT Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	ISOCITRIC ACID C₆ H₈ O₇ ODBLHEXUDAPZAU-ZAFYKAAXSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.257 (Depositor), 0.255 (DCC)
R-Value Work: 0.214 (Depositor), 0.211 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.774	α = 90
b = 206.162	β = 90.97
c = 145.598	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations

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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.