3KS7

Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 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 Putative PNGase FA, B, C, D397Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: BF0811BF9343_0774
Find proteins for Q5LH31 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343))
Explore Q5LH31 
Go to UniProtKB:  Q5LH31
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth C], E [auth A], F [auth A], JA [auth D], KA [auth D], P [auth B], Q [auth B]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth C] , FA [auth C] , GA [auth C] , HA [auth C] , IA [auth C] , J [auth A] , K [auth A] , L [auth A] , 
EA [auth C],  FA [auth C],  GA [auth C],  HA [auth C],  IA [auth C],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  MA [auth D],  N [auth A],  NA [auth D],  O [auth A],  OA [auth D],  PA [auth D],  QA [auth D],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth C] , CA [auth C] , DA [auth C] , G [auth A] , H [auth A] , I [auth A] , LA [auth D] , R [auth B] , 
BA [auth C],  CA [auth C],  DA [auth C],  G [auth A],  H [auth A],  I [auth A],  LA [auth D],  R [auth B],  S [auth B],  T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.057α = 90
b = 119.221β = 90
c = 154.314γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description