3GAG

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative NADH dehydrogenase, NADPH nitroreductaseA, B, C, D206Streptococcus mutansMutation(s): 0 
Gene Names: NP_720799.1SMU_346
UniProt
Find proteins for Q8DVW4 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q8DVW4 
Go to UniProtKB:  Q8DVW4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
E [auth A], K [auth B], P [auth C], T [auth D]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], U [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , L [auth B] , M [auth B] , N [auth B] , O [auth B] , 
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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 DOI: 10.18430/M33GAG Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.112α = 88.13
b = 52.478β = 80.35
c = 93.105γ = 62.14
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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