3LXQ

The Crystal Structure of a Protein in the Alkaline Phosphatase Superfamily from Vibrio parahaemolyticus to 1.95A

• PDB DOI: https://doi.org/10.2210/pdb3LXQ/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-25 Released: 2010-03-09 
• Deposition Author(s): Stein, A.J., Weger, A., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

The Crystal Structure of a Protein in the Alkaline Phosphatase Superfamily from Vibrio parahaemolyticus to 1.95A

Stein, A.J., Weger, A., Duggan, E., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.05 kDa 
• Atom Count: 6,672 
• Modelled Residue Count: 817 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein VP1736	A, B	450	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: VP1736
UniProt
Find proteins for Q87NY2 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87NY2  Go to UniProtKB:  Q87NY2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.95 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.603	α = 90
b = 164.521	β = 109.34
c = 50.929	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Stein, A.J., Weger, A., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary