2ZUL | pdb_00002zul

Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) in complex with cofactor S-adenosyl-L-Methionine

PDB DOI: https://doi.org/10.2210/pdb2ZUL/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-21 Released: 2009-10-27
Deposition Author(s): Wang, H., Kawazoe, M., Tatsuguchi, A., Naoe, C., Takemoto, C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.217 (Depositor), 0.217 (DCC)
R-Value Work:
0.183 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) in complex with cofactor S-adenosyl-L-Methionine

Wang, H., Kawazoe, M., Tatsuguchi, A., Naoe, C., Takemoto, C., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 41.11 kDa
Atom Count: 3,173
Modeled Residue Count: 372
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ribosomal RNA small subunit methyltransferase	A	375	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKW0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKW0 Go to UniProtKB: Q5SKW0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SKW0
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.217 (Depositor), 0.217 (DCC)
R-Value Work: 0.183 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.852	α = 90
b = 80.072	β = 90
c = 93.632	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2009-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, 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.