1WY7 | pdb_00001wy7

crystal structure of a putative RNA methyltransferase PH1948 from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb1WY7/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-08 Released: 2005-12-13 
• Deposition Author(s): Gao, Y.G., Yao, M., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.244 (DCC) 

Literature

Crystal structure of the putative RNA methyltransferase PH1948 from Pyrococcus horikoshii, in complex with the copurified S-adenosyl-L-homocysteine

Gao, Y.G., Yao, M., Yong, Z., Tanaka, I.

(2005) Proteins 61: 1141-1145

• PubMed: 16245322 
• DOI: https://doi.org/10.1002/prot.20678
• Primary Citation Related Structures: 
  1WY7

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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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.66 kDa 
• Atom Count: 6,823 
• Modeled Residue Count: 799 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PH1948	A, B, C, D	207	Pyrococcus horikoshii OT3	Mutation(s): 3  Gene Names: PH1948 EC: 2.1.1
UniProt
Find proteins for O59611 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59611  Go to UniProtKB:  O59611

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], F [auth B], G [auth C], H [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-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: 2.20 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.244 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 206.975	α = 90
b = 43.141	β = 92.08
c = 118.24	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-13 
Deposition Author(s): Gao, Y.G., Yao, M., Tanaka, I.

Revision History  

• Version 1.0: 2005-12-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary