7TCB | pdb_00007tcb

Crystal Structure of the YaeQ Family Protein VPA0551 from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb7TCB/pdb

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

Deposited: 2021-12-23 Released: 2022-01-05
Deposition Author(s): Kim, Y., Mulligan, R., Maltseva, N., Gu, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.265 (Depositor), 0.263 (DCC)
R-Value Work:
0.224 (Depositor), 0.222 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the YaeQ Family Protein VPA0551 from Vibrio parahaemolyticus

Kim, Y., Mulligan, R., Maltseva, N., Gu, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 85.5 kDa
Atom Count: 5,626
Modeled Residue Count: 692
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YaeQ family protein VPA0551	A, B, C, D	184	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VPA0551
UniProt
Find proteins for Q87IQ5 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87IQ5 Go to UniProtKB: Q87IQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87IQ5
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: 2.70 Å
R-Value Free: 0.265 (Depositor), 0.263 (DCC)
R-Value Work: 0.224 (Depositor), 0.222 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.024	α = 90
b = 47.687	β = 99.72
c = 115.519	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-05

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-01-05
Type: Initial release
Version 1.1: 2023-04-19
Changes: Database references, Structure summary
Version 1.2: 2024-11-13
Changes: Data collection, 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.