1WY7

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.268
R-Value Work: 0.242

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.20678
Primary Citation of Related Structures:
1WY7

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O59611
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.242
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-12-13

Deposition Author(s):

Gao, Y.G.

Yao, M.

Tanaka, I.

Revision History (Full details and data files)

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

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1WY7

crystal structure of a putative RNA methyltransferase PH1948 from Pyrococcus horikoshii

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)