1VCF | pdb_00001vcf

Crystal Structure of IPP isomerase at I422

• PDB DOI: https://doi.org/10.2210/pdb1VCF/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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Crystal Structure of IPP isomerase at I422

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 73.72 kDa 
• Atom Count: 4,569 
• Modeled Residue Count: 597 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isopentenyl-diphosphate delta-isomerase	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	D [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CD	C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

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: 2.60 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.427	α = 90
b = 144.427	β = 90
c = 169.821	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	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: 2024-10-09
  Changes: Structure summary