2R26

The Structure of the Ternary Complex of Carboxymethyl Coenzyme A and Oxalateacetate with Citrate Synthase from the Thermophilic Archaeonthermoplasma Acidophilum

PDB DOI: https://doi.org/10.2210/pdb2R26/pdb

Classification: TRANSFERASE
Organism(s): Thermoplasma acidophilum
Mutation(s): No

Deposited: 2007-08-24 Released: 2008-08-12
Deposition Author(s): Lehmann, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.261 (Depositor)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The Structure of the Ternary Complex of Carboxymethyl Coenzyme A and Oxalateacetate with Citrate Synthase from the Thermophilic Archaeonthermoplasma Acidophilum

Lehmann, C., Ellenberger, T.E., Kurz, L.C.

To be published.

Macromolecule Content

Total Structure Weight: 175.81 kDa
Atom Count: 13,168
Modelled Residue Count: 1,519
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate Synthase	A, B, C, D	384	Thermoplasma acidophilum	Mutation(s): 0 EC: 2.3.3.1 (PDB Primary Data), 2.3.3.16 (UniProt)
UniProt
Find proteins for P21553 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore P21553 Go to UniProtKB: P21553
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21553
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CMC Query on CMC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	*CARBOXYMETHYL COENZYME A** C₂₃ H₃₈ N₇ O₁₈ P₃ S OBUOSIHPWVNVJN-GRFIIANRSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
OAA Query on OAA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], I [auth C], K [auth D]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.261 (Depositor)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.705	α = 99.34
b = 74.221	β = 98.34
c = 89.874	γ = 114.38

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Lehmann, C.

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-04-03
Changes: Refinement description