8XU1 | pdb_00008xu1

DaCS-oxaloacetate complex

PDB DOI: https://doi.org/10.2210/pdb8XU1/pdb

Classification: TRANSFERASE
Organism(s): Desulfurella acetivorans A63
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-01-12 Released: 2025-01-22
Deposition Author(s): Yang, L., Fang, Y.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.258 (Depositor), 0.256 (DCC)
R-Value Work:
0.211 (Depositor), 0.217 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

DaCS-oxaloacetate complex

Yang, L., Fang, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 147.17 kDa
Atom Count: 10,421
Modeled Residue Count: 1,302
Deposited Residue Count: 1,305
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
citrate synthase	A, B, C	435	Desulfurella acetivorans A63	Mutation(s): 19 EC: 2.3.3.16
UniProt
Find proteins for A0A7C6A739 (Desulfurella acetivorans) Explore A0A7C6A739 Go to UniProtKB: A0A7C6A739
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7C6A739
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OAA (Subject of Investigation/LOI) Query on OAA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.258 (Depositor), 0.256 (DCC)
R-Value Work: 0.211 (Depositor), 0.217 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.1	α = 90
b = 111.28	β = 116.07
c = 99.56	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-01-22
Type: Initial release

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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.