2QM2 | pdb_00002qm2

Putative HopJ type III effector protein from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb2QM2/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-07-13 Released: 2007-07-31 
• Deposition Author(s): Kim, Y., Chang, C., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Putative HopJ type III Effector Protein from Vibrio parahaemolyticus.

Kim, Y., Chang, C., Volkart, L., Abdullah, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.65 kDa 
• Atom Count: 2,193 
• Modeled Residue Count: 234 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative HopJ type III effector protein	A, B	125	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 5  Gene Names: VPA0580
UniProt
Find proteins for Q87IM6 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87IM6  Go to UniProtKB:  Q87IM6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	F [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.622	α = 90
b = 90.886	β = 90
c = 72.445	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-31 
Deposition Author(s): Kim, Y., Chang, C., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-07-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary