3GAG

Crystal structure of a nitroreductase-like protein (smu.346) from streptococcus mutans at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GAG/pdb

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


• Deposited: 2009-02-17 Released: 2009-03-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.188 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

Crystal structure of nitroreductase-like protein (NP_720799.1) from Streptococcus mutans at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 98.74 kDa 
• Atom Count: 7,575 
• Modelled Residue Count: 820 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NADH dehydrogenase, NADPH nitroreductase	A, B, C, D	206	Streptococcus mutans	Mutation(s): 0  Gene Names: NP_720799.1, SMU_346
UniProt
Find proteins for Q8DVW4 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DVW4  Go to UniProtKB:  Q8DVW4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], K [auth B], P [auth C], T [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	F [auth A], U [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], V [auth D], W [auth D], X [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.188 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M33GAG

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.112	α = 88.13
b = 52.478	β = 80.35
c = 93.105	γ = 62.14

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations