Macromolecule Content

Total Structure Weight: 97.43 kDa
Atom Count: 6676
Modelled Residue Count: 768
Deposited Residue Count: 784
Unique protein chains: 1

3LCM

Crystal structure of Smu.1420 from Streptococcus mutans UA159

DOI: 10.2210/pdb3LCM/pdb

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

Deposited: 2010-01-11 Released: 2011-01-12
Deposition Author(s): Wang, Z.X., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.188
R-Value Work: 0.160
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and biochemical characterization of MdaB from cariogenic Streptococcus mutans reveals an NADPH-specific quinone oxidoreductase

Wang, Z.X., Li, L., Dong, Y.H., Su, X.-D.

(2014) Acta Crystallogr D Biol Crystallogr 70: 912-921

PubMed: 24699637 Search on PubMed
DOI: 10.1107/S1399004713033749
Primary Citation of Related Structures:
3LCM

PubMed Abstract:

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B, C, D	196	Streptococcus mutans UA159	Mutation(s): 0 Gene Names: smu.1420, SMU_1420 EC: 1.6.99.2 (PDB Primary Data), 1.6.5.2 (UniProt)
UniProt
Find proteins for Q8DTD1 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTD1 Go to UniProtKB: Q8DTD1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D]	E [auth A], G [auth B], I [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Ligand Interaction
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C]	F [auth A], H [auth B], J [auth C], K [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.188
R-Value Work: 0.160
R-Value Observed: 0.161
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.601	α = 90
b = 79.118	β = 90.01
c = 106.281	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2010-01-11
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: 2014-04-16
Changes: Database references
Version 1.3: 2017-10-04
Changes: Data collection

RCSB PDB is 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.