7WBR | pdb_00007wbr

Citrate synthase/lyase from Desulfurella acetivorans Desace_08345

• PDB DOI: https://doi.org/10.2210/pdb7WBR/pdb

• Classification: TRANSFERASE
• Organism(s): Desulfurella acetivorans
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): Yes 


• Deposited: 2021-12-17 Released: 2022-01-05 
• Deposition Author(s): Yang, L.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of Citrate synthase/lyase from Desulfurella acetivorans Desace_08345 complex with citrate

Yang, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 393.99 kDa 
• Atom Count: 27,573 
• Modeled Residue Count: 3,364 
• Deposited Residue Count: 3,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A, B, C, D, E, F, G, H	436	Desulfurella acetivorans	Mutation(s): 7  Gene Names: ENO40_01140 EC: 2.3.3.16

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 362.335	α = 90
b = 362.335	β = 90
c = 77.886	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-05 
Deposition Author(s): Yang, L.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2022-01-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description