5MDS

Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi in complex with chitotetraose

• PDB DOI: https://doi.org/10.2210/pdb5MDS/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Vibrio harveyi
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-11-13 Released: 2017-12-20 
• Deposition Author(s): Zahn, M., van den Berg, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.247 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.1 kDa 
• Atom Count: 8,166 
• Modelled Residue Count: 1,023 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitoporin	A, B, C	350	Vibrio harveyi	Mutation(s): 0  Gene Names: chiP Membrane Entity: Yes
UniProt
Find proteins for L0RVU0 (Vibrio harveyi) Explore L0RVU0  Go to UniProtKB:  L0RVU0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	4		N/A
Glycosylation Resources
GlyTouCan:  G01361SX GlyCosmos:  G01361SX GlyGen:  G01361SX

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.247 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 250.01	α = 90
b = 145.047	β = 94.8
c = 55.158	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Zahn, M., van den Berg, B.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary