1IXK

Crystal Structure Analysis of Methyltransferase Homolog Protein from Pyrococcus Horikoshii

• PDB DOI: https://doi.org/10.2210/pdb1IXK/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-06-25 Released: 2003-09-09 
• Deposition Author(s): Ishikawa, I., Sakai, N., Yao, M., Watanabe, N., Tamura, T., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.199 

Literature

Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii

Ishikawa, I., Sakai, N., Tamura, T., Yao, M., Watanabe, N., Tanaka, I.

(2004) Proteins 54: 814-816

• PubMed: 14997580 
• DOI: https://doi.org/10.1002/prot.10645
• Primary Citation of Related Structures:  
  1IXK

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Organizational Affiliation: 

Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.26 kDa 
• Atom Count: 2,586 
• Modelled Residue Count: 305 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A	315	Pyrococcus horikoshii	Mutation(s): 7  Gene Names: PH1374
UniProt
Find proteins for O50082 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O50082  Go to UniProtKB:  O50082

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.554	α = 90
b = 41.513	β = 114.18
c = 71.065	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
SHARP	phasing
WARP	model building
CNS	refinement
CCP4	data scaling
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-09 
Deposition Author(s): Ishikawa, I., Sakai, N., Yao, M., Watanabe, N., Tamura, T., Tanaka, I.

Revision History  

• Version 1.0: 2003-09-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations