3KR9

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase

PDB DOI: https://doi.org/10.2210/pdb3KR9/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-11-18 Released: 2009-12-22
Deposition Author(s): Ta, M.H., Kim, K.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.289
R-Value Work: 0.234
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase in complex with S-adenosyl-L-methionine

Ta, M.H., Kim, K.K.

To be published.

Macromolecule Content

Total Structure Weight: 24.97 kDa
Atom Count: 1,920
Modelled Residue Count: 222
Deposited Residue Count: 225
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent methyltransferase	A	225	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: SP_1610 EC: 2.1.1.36
UniProt
Find proteins for A0A0H2UR54 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UR54 Go to UniProtKB: A0A0H2UR54
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UR54
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.289
R-Value Work: 0.234
R-Value Observed: 0.236
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.807	α = 90
b = 58.668	β = 90
c = 142.995	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-12-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.