1K3R | pdb_00001k3r

Crystal Structure of the Methyltransferase with a Knot from Methanobacterium thermoautotrophicum

PDB DOI: https://doi.org/10.2210/pdb1K3R/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Methanothermobacter thermautotrophicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2001-10-03 Released: 2002-05-15
Deposition Author(s): Zarembinski, T.I., Kim, Y., Peterson, K., Christendat, D., Dharamsi, A., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.277 (Depositor), 0.238 (DCC)
R-Value Work:
0.221 (Depositor), 0.241 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1K3R

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

Literature

Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.

Zarembinski, T.I., Kim, Y., Peterson, K., Christendat, D., Dharamsi, A., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A.

(2003) Proteins 50: 177-183

PubMed: 12486711 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.10311
Primary Citation Related Structures:
1K3R

Organizational Affiliation

Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Macromolecule Content

Total Structure Weight: 60.47 kDa
Atom Count: 4,278
Modeled Residue Count: 526
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved protein MT0001	A, B	268	Methanothermobacter thermautotrophicus	Mutation(s): 0
UniProt
Find proteins for O26109 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26109 Go to UniProtKB: O26109
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26109
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.277 (Depositor), 0.238 (DCC)
R-Value Work: 0.221 (Depositor), 0.241 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.307	α = 90
b = 51.353	β = 94.69
c = 109.25	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-05-15

Deposition Author(s):

Zarembinski, T.I.

Christendat, D.

Arrowsmith, C.H.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2002-05-15
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references

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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.