3LD2 | pdb_00003ld2

The Crystal Structure of smu.2055 from Streptococcus mutans UA159

PDB DOI: https://doi.org/10.2210/pdb3LD2/pdb

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

Deposited: 2010-01-12 Released: 2011-01-12
Deposition Author(s): Su, X.-D., Zhan, X.R., Gao, X.Z., Liu, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.288 (Depositor), 0.261 (DCC)
R-Value Work:
0.225 (Depositor)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LD2

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of smu.2055 from Streptococcus mutans UA159

Su, X.-D., Zhan, X.R., Gao, X.Z., Liu, X.

To be published.

Macromolecule Content

Total Structure Weight: 92.97 kDa
Atom Count: 5,340
Modeled Residue Count: 638
Deposited Residue Count: 788
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetyltransferase	A, B, C, D	197	Streptococcus mutans UA159	Mutation(s): 0 Gene Names: smu.2055
UniProt
Find proteins for Q8DRZ8 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DRZ8 Go to UniProtKB: Q8DRZ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DRZ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.288 (Depositor), 0.261 (DCC)
R-Value Work: 0.225 (Depositor)
R-Value Observed: 0.229 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92	α = 90
b = 95	β = 90
c = 192.2	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

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: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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.