3B33

Crystal structure of the PAS domain of nitrogen regulation protein NR(II) from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb3B33/pdb

Classification: TRANSFERASE
Organism(s): Vibrio parahaemolyticus RIMD 2210633
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-10-19 Released: 2007-10-30
Deposition Author(s): Osipiuk, J., Sather, A., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.196 (Depositor), 0.197 (DCC)
R-Value Work:
0.184 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray structure of PAS domain of nitrogen regulation protein NR(II) from Vibrio parahaemolyticus.

Osipiuk, J., Sather, A., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 12.85 kDa
Atom Count: 981
Modelled Residue Count: 109
Deposited Residue Count: 115
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A	115	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VP0119 EC: 2.7.13.3
UniProt
Find proteins for Q87TF0 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87TF0 Go to UniProtKB: Q87TF0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87TF0
Sequence Annotations Expand
Reference Sequence LOADING

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: 1.83 Å
R-Value Free: 0.196 (Depositor), 0.197 (DCC)
R-Value Work: 0.184 (Depositor), 0.182 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.115	α = 90
b = 81.115	β = 90
c = 67.467	γ = 120

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
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-10-30

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-10-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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.