4GFR | pdb_00004gfr

Crystal Structure of the liganded Chitin Oligasaccharide Binding Protein

• PDB DOI: https://doi.org/10.2210/pdb4GFR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-03 Released: 2013-08-21 
• Deposition Author(s): Xu, S., Li, X., Gu, L., Roseman, R., Stock, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 

Literature

Chitin catabolic cascade in the marine bacterium Vibrio cholerae: properties, structure and functions of a periplasmic chitooligosaccharide binding protein (CBP)

Xu, S., Li, X., Gu, L., Roseman, R., Stock, A.M.

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: 60.5 kDa 
• Atom Count: 4,940 
• Modeled Residue Count: 529 
• Deposited Residue Count: 529 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide ABC transporter, periplasmic peptide-binding protein	A	529	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC0620, VC_0620
UniProt
Find proteins for Q9KUA3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KUA3  Go to UniProtKB:  Q9KUA3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.469	α = 90
b = 86.809	β = 90
c = 95.854	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Xu, S., Li, X., Gu, L., Roseman, R., Stock, A.M.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary