3LBY | pdb_00003lby

Crystal structure of SMU.1697c, a putative methyltransferase from streptococcus mutans in complex with SAH

PDB DOI: https://doi.org/10.2210/pdb3LBY/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus mutans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-08 Released: 2011-01-12
Deposition Author(s): Wang, K.-T., Nan, J., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.244 (Depositor), 0.250 (DCC)
R-Value Work:
0.210 (Depositor)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LBY

Ligand Structure Quality Assessment

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

Literature

Crystal structure of SMU.1697c, a putative methyltransferase from streptococcus mutans in complex with SAH

Wang, K.-T., Nan, J., Su, X.-D.

To be published.

Macromolecule Content

Total Structure Weight: 41.39 kDa
Atom Count: 2,773
Modeled Residue Count: 324
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein SMU.1697c	A, B	181	Streptococcus mutans	Mutation(s): 0 Gene Names: SMU_1697c
UniProt
Find proteins for Q8DSS3 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DSS3 Go to UniProtKB: Q8DSS3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DSS3
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.244 (Depositor), 0.250 (DCC)
R-Value Work: 0.210 (Depositor)
R-Value Observed: 0.212 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.21	α = 90
b = 92.21	β = 90
c = 107.01	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-05-30
Changes: Data collection
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.