1WG8 | pdb_00001wg8

Crystal structure of a predicted S-adenosylmethionine-dependent methyltransferase TT1512 from Thermus thermophilus HB8.

PDB DOI: https://doi.org/10.2210/pdb1WG8/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-05-27 Released: 2004-11-27
Deposition Author(s): Kishishita, S., Murayama, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.263 (Depositor)
R-Value Work:
0.216 (Depositor)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1WG8

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a predicted S-adenosylmethionine-dependent methyltransferase TT1512 from Thermus thermophilus HB8 at 2.0 Ang. resolution.

Kishishita, S., Murayama, K., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 63.24 kDa
Atom Count: 4,606
Modeled Residue Count: 561
Deposited Residue Count: 570
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
predicted S-adenosylmethionine-dependent methyltransferase	A, B	285	Thermus thermophilus	Mutation(s): 0 Gene Names: TT1512 EC: 2.1.1 (PDB Primary Data), 2.1.1.199 (UniProt)
UniProt
Find proteins for Q5SJD8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJD8 Go to UniProtKB: Q5SJD8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.263 (Depositor)
R-Value Work: 0.216 (Depositor)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.054	α = 90
b = 88.909	β = 90
c = 104.13	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-11-27

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2004-11-27
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.