2ZE9

Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of phospholipase D from streptomyces antibioticus

Suzuki, A.Toda, H.Iwasaki, Y.Yamane, T.Yamane, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase DA509Streptomyces antibioticusMutation(s): 1 
EC: 3.1.4.4
UniProt
Find proteins for Q53728 (Streptomyces antibioticus)
Explore Q53728 
Go to UniProtKB:  Q53728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53728
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PD7
Query on PD7

Download Ideal Coordinates CCD File 
C [auth A](2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate
C17 H33 O8 P
JAXUAGQDLYDLQB-OAHLLOKOSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
B [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.868α = 90
b = 78.232β = 90
c = 98.603γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations