3U07 | pdb_00003u07

Crystal Structure of the VPA0106 protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR106.

PDB DOI: https://doi.org/10.2210/pdb3U07/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-09-28 Released: 2011-10-12
Deposition Author(s): Vorobiev, S., Neely, H., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.216 (Depositor), 0.202 (DCC)
R-Value Work:
0.194 (Depositor), 0.179 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the VPA0106 protein from Vibrio parahaemolyticus.

Vorobiev, S., Neely, H., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 153.45 kDa
Atom Count: 10,329
Modeled Residue Count: 1,195
Deposited Residue Count: 1,329
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein VPA0106	A, B, C	443	Vibrio parahaemolyticus	Mutation(s): 2 Gene Names: VPA0106
UniProt
Find proteins for Q87JZ2 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87JZ2 Go to UniProtKB: Q87JZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87JZ2
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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.216 (Depositor), 0.202 (DCC)
R-Value Work: 0.194 (Depositor), 0.179 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.445	α = 60.61
b = 96.32	β = 80.87
c = 100.54	γ = 86.55

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary