2R9E | pdb_00002r9e

The structure of the binary complex of citryl dethia COA and citrate synthase from the thermophilic archaeonthermoplasma acidophilum

PDB DOI: https://doi.org/10.2210/pdb2R9E/pdb

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

Deposited: 2007-09-12 Released: 2008-09-30
Deposition Author(s): Lehmann, C., Chen, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.157 (Depositor), 0.157 (DCC)
R-Value Observed:
0.160 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Snapshots of Intermediates in the Condensation Reaction Catalyzed by Citrate Synthase

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

To be published.

Macromolecule Content

Total Structure Weight: 176.21 kDa
Atom Count: 13,585
Modeled Residue Count: 1,518
Deposited Residue Count: 1,540
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A, B, C, D	385	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21553
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SDX Query on SDX Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	s-citryldethia Coenzyme A C₂₈ H₄₆ N₇ O₂₂ P₃ JCKIRWYQPYQCEC-LWCHDFGBSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.215 (Depositor), 0.215 (DCC)
R-Value Work: 0.157 (Depositor), 0.157 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.061	α = 99.35
b = 73.498	β = 98.19
c = 89.983	γ = 113.89

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-30
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

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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.