2IRP

Crystal structure of the l-fuculose-1-phosphate aldolase (aq_1979) from aquifex aeolicus VF5

• PDB DOI: https://doi.org/10.2210/pdb2IRP/pdb

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


• Deposited: 2006-10-16 Released: 2007-10-30 
• Deposition Author(s): Jeyakanthan, J., Gayathri, D., Yogavel, M., Velmurugan, D., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.252 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal structure of the l-fuculose-1-phosphate aldolase (aq_1979) from aquifex aeolicus VF5

Jeyakanthan, J., Gayathri, D., Yogavel, M., Velmurugan, D., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 47.58 kDa 
• Atom Count: 3,630 
• Modelled Residue Count: 411 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aldolase class 2 protein aq_1979	A, B	208	Aquifex aeolicus VF5	Mutation(s): 0  EC: 4.1.2.17 (PDB Primary Data), 4.2.1.109 (UniProt)
UniProt
Find proteins for O67788 (Aquifex aeolicus (strain VF5)) Explore O67788  Go to UniProtKB:  O67788

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	D [auth A], F [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.252 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.5	α = 90
b = 102.5	β = 90
c = 116.045	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Jeyakanthan, J., Gayathri, D., Yogavel, M., Velmurugan, D., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance