3O5Y | pdb_00003o5y

The Crystal Structure of the GAF domain of a two-component sensor histidine kinase from Bacillus halodurans to 2.45A

PDB DOI: https://doi.org/10.2210/pdb3O5Y/pdb

Classification: transcription regulator
Organism(s): Halalkalibacterium halodurans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-28 Released: 2010-08-11
Deposition Author(s): Stein, A.J., Mack, J., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.269 (Depositor), 0.258 (DCC)
R-Value Work:
0.221 (Depositor)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3O5Y

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of the GAF domain of a two-component sensor histidine kinase from Bacillus halodurans to 2.45A

Stein, A.J., Mack, J., Buck, K., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 38.5 kDa
Atom Count: 2,328
Modeled Residue Count: 289
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A, B	165	Halalkalibacterium halodurans	Mutation(s): 0 Gene Names: cckA, BH0536 EC: 2.7.13.3
UniProt
Find proteins for Q9KFE5 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KFE5 Go to UniProtKB: Q9KFE5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KFE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B], E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.269 (Depositor), 0.258 (DCC)
R-Value Work: 0.221 (Depositor)
R-Value Observed: 0.223 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.961	α = 90
b = 96.961	β = 90
c = 104.695	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-08-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.