1YB2 | pdb_00001yb2

Structure of a putative methyltransferase from Thermoplasma acidophilum.

PDB DOI: https://doi.org/10.2210/pdb1YB2/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Thermoplasma acidophilum DSM 1728
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-12-18 Released: 2005-02-01
Deposition Author(s): Cuff, M.E., Xu, X., Edwards, A., Savchenko, A., Sanishvili, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.247 (Depositor), 0.248 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YB2

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

Literature

Structure of a putative methyltransferase from Thermoplasma acidophilum.

Cuff, M.E., Xu, X., Edwards, A., Savchenko, A., Sanishvili, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 31.19 kDa
Atom Count: 1,918
Modeled Residue Count: 230
Deposited Residue Count: 275
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein Ta0852	A	275	Thermoplasma acidophilum DSM 1728	Mutation(s): 11 Gene Names: Ta0852
UniProt
Find proteins for Q9HJW1 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HJW1 Go to UniProtKB: Q9HJW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HJW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.247 (Depositor), 0.248 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.316	α = 90
b = 60.557	β = 105.12
c = 65.841	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-02-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-02-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.