3E3X | pdb_00003e3x

The C-terminal part of BipA protein from Vibrio parahaemolyticus RIMD 2210633

• PDB DOI: https://doi.org/10.2210/pdb3E3X/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-08 Released: 2008-09-30 
• Deposition Author(s): Nocek, B., Mulligan, R., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.223 (Depositor) 
• R-Value Work: 
  0.172 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

The C-terminal part of BipA protein from Vibrio parahaemolyticus RIMD 2210633

Nocek, B., Mulligan, R., Duggan, E., Clancy, S., 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)

Macromolecule Content 

• Total Structure Weight: 37.64 kDa 
• Atom Count: 2,485 
• Modeled Residue Count: 286 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BipA	A	332	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: bipA, VP0122 EC: 3.6.5
UniProt
Find proteins for Q9L5X8 (Vibrio parahaemolyticus) Explore Q9L5X8  Go to UniProtKB:  Q9L5X8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MLZ	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS
MSE	A	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:  0.223 (Depositor) 
• R-Value Work:  0.172 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.6	α = 90
b = 104.571	β = 90
c = 74.348	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
ARP	model building
Coot	model building
MLPHARE	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Nocek, B., Mulligan, R., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary