5Z7H

Crystal structure of CcpE regulatory domain in citrate-bound form from Staphyloccocus aureus

• PDB DOI: https://doi.org/10.2210/pdb5Z7H/pdb

• Classification: TRANSCRIPTION
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-01-28 Released: 2018-02-28 
• Deposition Author(s): Chen, J., Wang, L., Shang, F., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.247 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5ZZO

Literature

Citrate-responsive mechanism of catabolite control protein E from Staphyloccocus aureus

Chen, J., Wang, L., Shang, F., Xu, Y.

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 Evidence: gel filtration

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)

Macromolecule Content

• Total Structure Weight: 200.82 kDa 
• Atom Count: 10,604 
• Modelled Residue Count: 1,167 
• Deposited Residue Count: 1,728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR family transcriptional regulator	A, B, C, D, E, F	288	Staphylococcus aureus	Mutation(s): 0  Gene Names: QU38_10390
UniProt
Find proteins for A0A0D1IHL7 (Staphylococcus aureus) Explore A0A0D1IHL7  Go to UniProtKB:  A0A0D1IHL7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.247 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.788	α = 90
b = 111.658	β = 95.14
c = 152.971	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Chen, J., Wang, L., Shang, F., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
National Natural Science Foundation of China	China	21272031

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references