2Z95 | pdb_00002z95

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

• PDB DOI: https://doi.org/10.2210/pdb2Z95/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-18 Released: 2008-03-18 
• Deposition Author(s): Niwa, H., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

Niwa, H., Kuramitsu, S., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 158.74 kDa 
• Atom Count: 10,913 
• Modeled Residue Count: 1,335 
• Deposited Residue Count: 1,380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-D-mannose dehydratase	A, B, C, D	345	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: rfbD EC: 4.2.1.47
UniProt
Find proteins for O67175 (Aquifex aeolicus (strain VF5)) Explore O67175  Go to UniProtKB:  O67175

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
GDP	F [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.482	α = 90
b = 101.178	β = 90
c = 186.242	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Niwa, H., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description