3BEM

Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative NAD(P)H nitroreductase ydfN
A, B
218Bacillus subtilis (strain 168)Mutation(s): 3 
Gene Names: mhqN (ydfN)
EC: 1.-.-.-
Find proteins for P96692 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P96692
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

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Download CCD File 
A, B
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 51.620α = 90.00
b = 69.200β = 100.54
c = 61.850γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
XSCALEdata scaling
PHENIXrefinement
REFMACrefinement
MolProbitymodel building
XDSdata reduction
MAR345data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description