5Z72

Crystal structure of CcpC regulatory domain in complex with citrate from Bacillus amyloliquefaciens

PDB DOI: https://doi.org/10.2210/pdb5Z72/pdb

Classification: TRANSCRIPTION
Organism(s): Bacillus velezensis FZB42
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2018-01-26 Released: 2018-02-28
Deposition Author(s): Chen, J., Wang, L., Shang, F., Xu, Y.
Funding Organization(s): National Natural Science Foundation of China, Program for Liaoning Excellent Talents in University

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.255
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Mechanistic insights from the crystal structures of a catabolite control protein C on citrate-responsive mechanism

Chen, J., Wang, L., Dong, Y., Ha, N.C.

To be published.

Macromolecule Content

Total Structure Weight: 171.38 kDa
Atom Count: 8,239
Modelled Residue Count: 963
Deposited Residue Count: 1,465
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CcpC	A, B, C, D, E	293	Bacillus velezensis FZB42	Mutation(s): 0 Gene Names: ccpC, RBAM_013910
UniProt
Find proteins for A7Z428 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42)) Explore A7Z428 Go to UniProtKB: A7Z428
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7Z428
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E]	H [auth A], L [auth B], O [auth C], T [auth D], V [auth E]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain V [auth E] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain V [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth D], S [auth D], U [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.255
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.963	α = 90
b = 90.898	β = 106.18
c = 105.531	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	Grant No. 31200556
National Natural Science Foundation of China	China	21272031
Program for Liaoning Excellent Talents in University	China	LJQ2015030

Revision History (Full details and data files)

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

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Help and Resources

5Z72

Crystal structure of CcpC regulatory domain in complex with citrate from Bacillus amyloliquefaciens

Mechanistic insights from the crystal structures of a catabolite control protein C on citrate-responsive mechanism

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)