4ONX | pdb_00004onx

2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase from Clostridium perfringens.

PDB DOI: https://doi.org/10.2210/pdb4ONX/pdb

Classification: TRANSFERASE
Organism(s): Clostridium perfringens ATCC 13124
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-01-29 Released: 2014-03-05
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kwon, K., Shatsman, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.250 (Depositor), 0.254 (DCC)
R-Value Work:
0.197 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

2.8 Angstrom Crystal Structure of Sensor Domain of Histidine Kinase from Clostridium perfringens.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kwon, K., Shatsman, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 115.5 kDa
Atom Count: 6,328
Modeled Residue Count: 765
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor histidine kinase	A, B, C, D, E A, B, C, D, E, F	162	Clostridium perfringens ATCC 13124	Mutation(s): 0 Gene Names: CPF_0511
UniProt
Find proteins for A0A0H2YV09 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YV09 Go to UniProtKB: A0A0H2YV09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2YV09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], N [auth C], P [auth D], Q [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth D] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth D] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.250 (Depositor), 0.254 (DCC)
R-Value Work: 0.197 (Depositor), 0.201 (DCC)
R-Value Observed: 0.200 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.903	α = 90
b = 82.739	β = 105.92
c = 73.954	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-05

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-03-05
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary