2VMG

The structure of CBM51 from Clostridium perfringens GH95 in complex with methyl-galactose

• PDB DOI: https://doi.org/10.2210/pdb2VMG/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-01-25 Released: 2008-02-19 
• Deposition Author(s): Gregg, K., Finn, R., Abbott, D.W., Boraston, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.296 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 17.1 kDa 
• Atom Count: 1,260 
• Modelled Residue Count: 145 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBRONECTIN TYPE III DOMAIN PROTEIN	A	157	Clostridium perfringens	Mutation(s): 0
UniProt
Find proteins for A0A0H2YQB3 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YQB3  Go to UniProtKB:  A0A0H2YQB3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBG	C [auth A]	methyl beta-D-galactopyranoside C7 H14 O6 HOVAGTYPODGVJG-VOQCIKJUSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MBG	Binding MOAD:  2VMG	Ka: 480 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.296 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.475	α = 90
b = 47.948	β = 92
c = 38.704	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Gregg, K., Finn, R., Abbott, D.W., Boraston, A.B.

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-09-25
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary