1VCG | pdb_00001vcg

Crystal Structure of IPP isomerase at P43212

• PDB DOI: https://doi.org/10.2210/pdb1VCG/pdb

• Classification: ISOMERASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-03-08 Released: 2005-04-19 
• Deposition Author(s): Wada, T., Park, S.-Y., Tame, R.H., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.262 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Crystal Structure of IPP isomerase at P43212

Wada, T., Park, S.-Y., Tame, R.H., Kuramitsu, S., Yokoyama, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 147.22 kDa 
• Atom Count: 9,677 
• Modeled Residue Count: 1,256 
• Deposited Residue Count: 1,328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isopentenyl-diphosphate delta-isomerase	A, B, C, D	332	Thermus thermophilus	Mutation(s): 6  EC: 5.3.3.2
UniProt
Find proteins for Q746I8 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q746I8  Go to UniProtKB:  Q746I8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.262 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.953	α = 90
b = 112.953	β = 90
c = 261.283	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-19 
Deposition Author(s): Wada, T., Park, S.-Y., Tame, R.H., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary