7ETS | pdb_00007ets

Crystal structure of crp protein from Gardnerella Vaginalis

• PDB DOI: https://doi.org/10.2210/pdb7ETS/pdb

• Classification: TRANSCRIPTION
• Organism(s): Gardnerella vaginalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-13 Released: 2022-04-27 
• Deposition Author(s): Dong, H.J., Wang, S., Zhang, J.M., Gu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of crp protein from Gardnerella Vaginalis

Dong, H.J., Wang, S., Zhang, J.M., Gu, 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)

Macromolecule Content 

• Total Structure Weight: 51.88 kDa 
• Atom Count: 3,692 
• Modeled Residue Count: 443 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crp/Fnr family transcriptional regulator	A, B	226	Gardnerella vaginalis	Mutation(s): 0  Gene Names: AXE75_06165, CG405_03440, CYJ58_00485, CYJ65_00490, CYJ68_02605, EGX90_02820

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.953	α = 90
b = 85.471	β = 116.685
c = 56.022	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Dong, H.J., Wang, S., Zhang, J.M., Gu, L.

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

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description