4LGO | pdb_00004lgo

Crystal Structure of N-terminal domain 1 of VompD from Bartonella quintana

• PDB DOI: https://doi.org/10.2210/pdb4LGO/pdb

• Classification: CELL ADHESION
• Organism(s): Bartonella quintana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-28 Released: 2014-03-05 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.188 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of N-terminal domain 1 of VompD from Bartonella quintana

Dranow, D.M., Abendroth, J., Edwards, T.E., Lorimer, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 43.99 kDa 
• Atom Count: 2,891 
• Modeled Residue Count: 353 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VompD	A, B, C	136	Bartonella quintana	Mutation(s): 0  Gene Names: vompD
UniProt
Find proteins for A0A0H3LUZ2 (Bartonella quintana (strain Toulouse)) Explore A0A0H3LUZ2  Go to UniProtKB:  A0A0H3LUZ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth B], E [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.188 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34LGO

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.03	α = 90
b = 37.11	β = 119.43
c = 109.78	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2025-10-22
  Changes: Structure summary