4MH6 | pdb_00004mh6

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34mh6

Space Group: I 4₁ 2 2

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary