5IR0 | pdb_00005ir0

Crystal structure of protein of unknown function ORF19 from Vibrio cholerae O1 PICI-like element, C57S I109M mutant

PDB DOI: https://doi.org/10.2210/pdb5IR0/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Vibrio cholerae O1 biovar El Tor
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-03-11 Released: 2016-03-30
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Skarina, T., Di Leo, R., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.293 (Depositor), 0.296 (DCC)
R-Value Work:
0.237 (Depositor), 0.242 (DCC)
R-Value Observed:
0.243 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5IR0

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

Literature

Crystal structure of protein of unknown function ORF19 from Vibrio cholerae O1 PICI-like element, C57S I109M mutant

Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 36.87 kDa
Atom Count: 1,683
Modeled Residue Count: 205
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ORF19	A, B	161	Vibrio cholerae O1 biovar El Tor	Mutation(s): 2
UniProt
Find proteins for M1Q7T5 (Vibrio cholerae serotype O1 biovar El Tor) Explore M1Q7T5 Go to UniProtKB: M1Q7T5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1Q7T5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.293 (Depositor), 0.296 (DCC)
R-Value Work: 0.237 (Depositor), 0.242 (DCC)
R-Value Observed: 0.243 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.852	α = 90
b = 126.852	β = 90
c = 51.62	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-03-30
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.