3B33 | pdb_00003b33

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

Validation slider image for 3B33

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
Modeled Residue Count: 109
Deposited Residue Count: 115
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87TF0
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: 1.83 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

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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

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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.