1YLN | pdb_00001yln

The Crystal Structure of the Protein of Unknown Function VCA0042 from Vibrio cholerae O1

PDB DOI: https://doi.org/10.2210/pdb1YLN/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Vibrio cholerae O1
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2005-01-19 Released: 2005-03-08
Deposition Author(s): Zhang, R., Zhou, M., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.243 (Depositor), 0.253 (DCC)
R-Value Work:
0.210 (Depositor), 0.221 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YLN

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

Literature

The crystal structure of the hypothetical protein vca0042 from Vibrio cholerae O1

Zhang, R., Zhou, M., Moy, S., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 28.5 kDa
Atom Count: 1,928
Modeled Residue Count: 226
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein vca0042	A	252	Vibrio cholerae O1	Mutation(s): 1 Gene Names: GI:9657424
UniProt
Find proteins for Q9KNC3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KNC3 Go to UniProtKB: Q9KNC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KNC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OSE Query on OSE	A	L-PEPTIDE LINKING	C₃ H₇ N O₆ S		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.243 (Depositor), 0.253 (DCC)
R-Value Work: 0.210 (Depositor), 0.221 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.429	α = 90
b = 56.429	β = 90
c = 171.128	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-03-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-03-08
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-06
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.