3LDF | pdb_00003ldf

Crystal structure of SMU.776, a putative methyltransferase complexed with SAH

PDB DOI: https://doi.org/10.2210/pdb3LDF/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., Nan, J., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.232 (Depositor), 0.253 (DCC)
R-Value Work:
0.173 (Depositor), 0.191 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3LDF

Ligand Structure Quality Assessment

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

Literature

Crystal structure of SMU.776 complexed with SAH

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

To be published.

Macromolecule Content

Total Structure Weight: 44.12 kDa
Atom Count: 3,284
Modeled Residue Count: 380
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein SMU.776	A	385	Streptococcus mutans UA159	Mutation(s): 0 Gene Names: SMU_776
UniProt
Find proteins for Q8DUW5 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DUW5 Go to UniProtKB: Q8DUW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DUW5
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] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.232 (Depositor), 0.253 (DCC)
R-Value Work: 0.173 (Depositor), 0.191 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.684	α = 90
b = 50.828	β = 107.14
c = 59.569	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-01-19

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
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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.