3HDV | pdb_00003hdv

Crystal structure of response regulator receiver protein from Pseudomonas putida

PDB DOI: https://doi.org/10.2210/pdb3HDV/pdb

Classification: transcription regulator
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-07 Released: 2009-05-26
Deposition Author(s): Bagaria, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.245 (Depositor), 0.253 (DCC)
R-Value Work:
0.205 (Depositor), 0.218 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3HDV

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

Literature

Crystal structure of response regulator receiver protein from Pseudomonas putida

Bagaria, A., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 60.96 kDa
Atom Count: 3,978
Modeled Residue Count: 484
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator	A, B, C, D	136	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: PP_0355, PP0355
UniProt
Find proteins for Q88QX9 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88QX9 Go to UniProtKB: Q88QX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88QX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.245 (Depositor), 0.253 (DCC)
R-Value Work: 0.205 (Depositor), 0.218 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.769	α = 90
b = 140.436	β = 90
c = 48.571	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Database references, 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.