3H7M | pdb_00003h7m

Crystal Structure of a Histidine Kinase Sensor Domain with Similarity to Periplasmic Binding Proteins

PDB DOI: https://doi.org/10.2210/pdb3H7M/pdb

Classification: TRANSFERASE
Organism(s): Geobacter sulfurreducens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-27 Released: 2009-06-30
Deposition Author(s): Cheung, J., Le-Khac, M., Hendrickson, W.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.285 (Depositor), 0.226 (DCC)
R-Value Work:
0.228 (Depositor), 0.236 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 3H7M

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

Literature

Crystal structure of a histidine kinase sensor domain with similarity to periplasmic binding proteins.

Cheung, J., Le-Khac, M., Hendrickson, W.A.

(2009) Proteins 77: 235-241

PubMed: 19544572 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.22485
Primary Citation Related Structures:
3H7M

Organizational Affiliation

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Macromolecule Content

Total Structure Weight: 25.98 kDa
Atom Count: 1,951
Modeled Residue Count: 228
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A	234	Geobacter sulfurreducens	Mutation(s): 0 Gene Names: GSU2755 EC: 2.7.13.3
UniProt
Find proteins for Q749I7 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q749I7 Go to UniProtKB: Q749I7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q749I7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.285 (Depositor), 0.226 (DCC)
R-Value Work: 0.228 (Depositor), 0.236 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.92	α = 90
b = 122.92	β = 90
c = 81.692	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Hendrickson, W.A.

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.