4M88 | pdb_00004m88

Crystal structure of extracellular ligand-binding receptor from Verminephrobacter eiseniae ef01-2

• PDB DOI: https://doi.org/10.2210/pdb4M88/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Verminephrobacter eiseniae EF01-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-13 Released: 2013-11-06 
• Deposition Author(s): Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of extracellular ligand-binding receptor from Verminephrobacter eiseniae ef01-2

Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 38.17 kDa 
• Atom Count: 2,734 
• Modeled Residue Count: 355 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular ligand-binding receptor	A	357	Verminephrobacter eiseniae EF01-2	Mutation(s): 0  Gene Names: Veis_2660
UniProt
Find proteins for A1WL96 (Verminephrobacter eiseniae (strain EF01-2)) Explore A1WL96  Go to UniProtKB:  A1WL96

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.76 Å
• R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.076	α = 90
b = 95.81	β = 111.56
c = 50.3	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Data collection
• Version 1.2: 2013-12-18
  Changes: Structure summary
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2025-10-22
  Changes: Database references, Structure summary