1VKO | pdb_00001vko

Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VKO/pdb

• Classification: ISOMERASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-11 Released: 2004-08-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 61.21 kDa 
• Atom Count: 4,217 
• Modeled Residue Count: 511 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
inositol-3-phosphate synthase	A	537	Caenorhabditis elegans	Mutation(s): 0  Gene Names: ce21227 EC: 5.5.1.4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
POP	H [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
IOD	E [auth A], F [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VKO

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.98	α = 90
b = 129.98	β = 90
c = 131.32	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
autoSHARP	phasing
REFMAC	refinement
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Data collection, Refinement description