1YZH | pdb_00001yzh

Crystal Structure of the Conserved Hypothetical Protein, Methyltransferase from Streptococcus pneumoniae TIGR4

PDB DOI: https://doi.org/10.2210/pdb1YZH/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-02-28 Released: 2005-04-12
Deposition Author(s): Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.208 (Depositor), 0.207 (DCC)
R-Value Work:
0.179 (Depositor), 0.177 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YZH

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

Literature

Crystal Structure of the Conserved Methyltransferase from Streptococcus pneumoniae TIGR4

Kim, Y., Li, H., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 49.83 kDa
Atom Count: 3,725
Modeled Residue Count: 410
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(7)-)-methyltransferase	A, B	214	Streptococcus pneumoniae	Mutation(s): 4 Gene Names: trmB, SP0550 EC: 2.1.1.33
UniProt
Find proteins for P67506 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P67506 Go to UniProtKB: P67506
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67506
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.208 (Depositor), 0.207 (DCC)
R-Value Work: 0.179 (Depositor), 0.177 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.613	α = 90
b = 41.253	β = 111.87
c = 78.658	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-04-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-04-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2024-10-09
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.