3LDG

Crystal structure of SMU.472, a putative methyltransferase complexed with SAH

PDB DOI: https://doi.org/10.2210/pdb3LDG/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus mutans UA159
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-13 Released: 2011-01-19
Deposition Author(s): Wang, K.-T., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.245
R-Value Work: 0.188
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of SMU.472 complexed with SAH

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

To be published.

Macromolecule Content

Total Structure Weight: 44.4 kDa
Atom Count: 3,392
Modelled Residue Count: 377
Deposited Residue Count: 384
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein SMU.472	A	384	Streptococcus mutans UA159	Mutation(s): 0 Gene Names: SMU_472
UniProt
Find proteins for Q8DVL0 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DVL0 Go to UniProtKB: Q8DVL0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DVL0
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]	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]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.245
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.251	α = 90
b = 67.348	β = 90
c = 91.848	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

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.