3JX8

Crystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides distasonis ATCC 8503 at 2.16 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 lipoproteinA, B, C, D, E, F250Parabacteroides distasonis ATCC 8503Mutation(s): 0 
Gene Names: BDI_3087YP_001304415.1
Find proteins for A6LGH9 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152))
Explore A6LGH9 
Go to UniProtKB:  A6LGH9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth D] , FA [auth D] , G [auth A] , GA [auth D] , H [auth A] , I [auth A] , JA [auth E] , KA [auth E] , 
EA [auth D],  FA [auth D],  G [auth A],  GA [auth D],  H [auth A],  I [auth A],  JA [auth E],  KA [auth E],  LA [auth E],  N [auth B],  O [auth B],  P [auth B],  PA [auth F],  Q [auth B],  QA [auth F],  R [auth B],  RA [auth F],  X [auth C],  Y [auth C],  Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , HA [auth D] , IA [auth D] , J [auth A] , K [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  HA [auth D],  IA [auth D],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  MA [auth E],  NA [auth E],  OA [auth E],  SA [auth F],  T [auth B],  TA [auth F],  U [auth B],  UA [auth F],  V [auth B],  W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
S [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.88α = 90
b = 201.88β = 90
c = 202.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description