2ZBQ | pdb_00002zbq

Crystal structure of ribosomal protein L11 methyltransferase from Thermus thermophilus in complex with S-adenosyl-L-homocysteine

PDB DOI: https://doi.org/10.2210/pdb2ZBQ/pdb

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

Deposited: 2007-10-26 Released: 2008-11-11
Deposition Author(s): Kaminishi, T., Sakai, H., Takemoto-Hori, C., Terada, T., Nakagawa, N., Maoka, N., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.292 (Depositor), 0.270 (DCC)
R-Value Work:
0.241 (Depositor), 0.221 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of ribosomal protein L11 methyltransferase from Thermus thermophilus

Kaminishi, T., Sakai, H., Takemoto-Hori, C., Terada, T., Nakagawa, N., Maoka, N., Kuramitsu, S., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 28.05 kDa
Atom Count: 2,032
Modeled Residue Count: 251
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L11 methyltransferase	A	254	Thermus thermophilus	Mutation(s): 0 Gene Names: prmA EC: 2.1.1
UniProt
Find proteins for Q84BQ9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q84BQ9 Go to UniProtKB: Q84BQ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84BQ9
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.292 (Depositor), 0.270 (DCC)
R-Value Work: 0.241 (Depositor), 0.221 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.912	α = 90
b = 75.685	β = 130.95
c = 61.931	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-11-11

Deposition Author(s):

Takemoto-Hori, C.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-11-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.