4QPR | pdb_00004qpr

CRYSTAL STRUCTURE OF GAF DOMAIN of POTASSIUM SENSOR HISTIDINE KINASE KDPD FROM ESCHERICHIA COLI

PDB DOI: https://doi.org/10.2210/pdb4QPR/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-24 Released: 2015-09-02
Deposition Author(s): Kumar, S., Yernool, D.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.185 (Depositor), 0.187 (DCC)
R-Value Observed:
0.187 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Gaf Domain of Potassium Sensor Histidine Kinase Kdpd from Escherichia Coli

Kumar, S., Yernool, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 16.51 kDa
Atom Count: 1,179
Modeled Residue Count: 142
Deposited Residue Count: 149
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein KdpD	A	149	Escherichia coli K-12	Mutation(s): 0 Gene Names: b0695, ECDH1ME8569_0654, EcDH1_2941, JW0683, kdpD EC: 2.7.13.3
UniProt
Find proteins for P21865 (Escherichia coli (strain K12)) Explore P21865 Go to UniProtKB: P21865
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21865
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.203 (Depositor), 0.203 (DCC)
R-Value Work: 0.185 (Depositor), 0.187 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.31	α = 90
b = 57.61	β = 90
c = 61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-02
Type: Initial release
Version 1.1: 2024-10-30
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.