3CIN | pdb_00003cin

CRYSTAL STRUCTURE OF A MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN (TM_1419) FROM THERMOTOGA MARITIMA MSB8 AT 1.70 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3CIN/pdb
• Entry: 3CIN supersedes: 1VJP

• Classification: ISOMERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-11 Released: 2008-03-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.194 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MYO-inositol-1-phosphate synthase-related protein (TM1419) from Thermotoga maritima at 1.70 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 (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 44.5 kDa 
• Atom Count: 3,311 
• Modeled Residue Count: 382 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myo-inositol-1-phosphate synthase-related protein	A	394	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM1419, TM_1419 EC: 5.5.1.4
UniProt
Find proteins for Q9X1D6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1D6  Go to UniProtKB:  Q9X1D6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.194 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CIN

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.304	α = 90
b = 104.95	β = 90
c = 117.013	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 1VJP

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description