3GBH

CRYSTAL STRUCTURE OF A PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE (SE1966) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 2.00 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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 putative NAD(P)H:FMN oxidoreductase (NP_765521.1) from Staphylococcus epidermidis ATCC 12228 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-flavin oxidoreductaseA, B, C, D213Staphylococcus epidermidis ATCC 12228Mutation(s): 0 
Gene Names: NP_765521.1SE_1966
UniProt
Find proteins for A0A0H2VHN8 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200))
Explore A0A0H2VHN8 
Go to UniProtKB:  A0A0H2VHN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2VHN8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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

Download Ideal Coordinates CCD File 
L [auth B],
V [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
K [auth B],
Q [auth C],
R [auth C],
G [auth A],
J [auth B],
K [auth B],
Q [auth C],
R [auth C],
U [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B],
W [auth D],
X [auth D],
Y [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
P [auth C],
T [auth D]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.85α = 90
b = 86.15β = 90
c = 160.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    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