7ANI | pdb_00007ani

DdahB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni

• PDB DOI: https://doi.org/10.2210/pdb7ANI/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-10-11 Released: 2020-10-21 
• Deposition Author(s): Naismith, J.H., Woodward, L.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

DdahB

Naismith, J.H., Woodward, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.1 kDa 
• Atom Count: 3,191 
• Modeled Residue Count: 348 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine diphospho-4-keto-rhamnose 3,5-epimerase	A, B	183	Campylobacter jejuni	Mutation(s): 0  Gene Names:  BBR99_05345, D0W34_08620, D5I02_08520, F0H18_08555, F1P94_09915, FRS42_06315, FVZ69_07850, FW031_08545, FW918_03925, FWZ96_07945, GAX04_08395, GJ442_08190, GRS20_08795, GSH24_04195, GY415_001377, GZD82_001464, HS23.15 EC: 5.1.3.13
UniProt
Find proteins for Q6EF58 (Campylobacter jejuni) Explore Q6EF58  Go to UniProtKB:  Q6EF58

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.75	α = 90
b = 68.19	β = 91.36
c = 53.67	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Naismith, J.H., Woodward, L.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100209/Z/12/Z)

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description