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)

Experimental Data Snapshot

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

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of crp protein from Gardnerella Vaginalis

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

To be published.

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

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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	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-27

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

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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.