4MH6

2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb4MH6/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Vibrio parahaemolyticus RIMD 2210633
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2013-08-29 Released: 2013-09-11
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Winsor, J., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.243
R-Value Work: 0.189
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

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

Literature

2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO from Vibrio parahaemolyticus.

Minasov, G., Wawrzak, Z., Shuvalova, L., Winsor, J., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 21.51 kDa
Atom Count: 1,478
Modelled Residue Count: 159
Deposited Residue Count: 177
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative type III secretion protein YscO	A	177	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VP1669, yscO
UniProt
Find proteins for Q87P49 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87P49 Go to UniProtKB: Q87P49
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87P49
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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: 2.80 Å
R-Value Free: 0.243
R-Value Work: 0.189
R-Value Observed: 0.192
Space Group: I 4₁ 2 2
Diffraction Data: https://doi.org/10.18430/M34MH6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.114	α = 90
b = 149.114	β = 90
c = 63.422	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SHELXS	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.