6LFD | pdb_00006lfd

Crystal structure of VMB-1 at pH5.5(Bis-Tris)

• PDB DOI: https://doi.org/10.2210/pdb6LFD/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio alginolyticus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-12-02 Released: 2020-02-26 
• Deposition Author(s): Cheng, Q., Chen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of VMB-1 at pH 5.5(Bis-Tris)

Chen, S., Cheng, Q.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 103.53 kDa 
• Atom Count: 7,203 
• Modeled Residue Count: 877 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VMB-1	A, B, C, D	234	Vibrio alginolyticus	Mutation(s): 0  Gene Names: vmb-1 EC: 3.5.2.6
UniProt
Find proteins for A0A5Q5ADH9 (Vibrio alginolyticus) Explore A0A5Q5ADH9  Go to UniProtKB:  A0A5Q5ADH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], K [auth C], L [auth C], M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.11	α = 90
b = 97.11	β = 90
c = 132.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Cheng, Q., Chen, S.

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2020-03-18
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description