1MKT

CARBOXYLIC ESTER HYDROLASE, 1.72 ANGSTROM TRIGONAL FORM OF THE BOVINE RECOMBINANT PLA2 ENZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

1.72 A resolution refinement of the trigonal form of bovine pancreatic phospholipase A2.

Sekar, K.Sekharudu, C.Tsai, M.D.Sundaralingam, M.

(1998) Acta Crystallogr.,Sect.D 54: 342-346


  • PubMed Abstract: 
  • The trigonal crystal structure of the recombinant bovine pancreatic phospholipase A2 has been re-refined at a slightly higher resolution (1.72 A). The crystals are trigonal, space group P3121, unit-cell parameters a = b = 46.78 and c = 102.89 A and a ...

    The trigonal crystal structure of the recombinant bovine pancreatic phospholipase A2 has been re-refined at a slightly higher resolution (1.72 A). The crystals are trigonal, space group P3121, unit-cell parameters a = b = 46.78 and c = 102.89 A and are isomorphous to the previous structure. The structure was refined to a final crystallographic R value of 19.5% (Rfree = 28.4%) using 10 531 reflections. A total of 106 solvent molecules were included in the refinement compared with the earlier refinement which contains only 85 water molecules and 8 925 reflections at 1.8 A resolution. The root-mean-square deviation from the ideal bond lengths and bond angles is considerably better in the present refinement. The active site is extended ( approximately 14 A) from Ala1 to the calcium. The three catalytic residues (Asp99, His48 and the catalytic water) are connected by the conserved structural water and the N-terminal Ala1 on one side, and by the calcium through an equatorial water on the other. The water molecules play a role in the activity of the enzyme PLA2. The Ala1 end of the extended active site performs the activation of the phospholid membranes while the opposite end performs the hydrolysis of the monomeric phospholids.


    Related Citations: 
    • Phospholipase A2 Engineering. Deletion of the C-Terminus Segment Changes Substrate Specificity and Uncouples Calcium and Substrate Binding at the Zwitterionic Interface
      Huang, B.,Yu, B.Z.,Rogers, J.,Byeon, I.J.,Sekar, K.,Chen, X.,Sundaralingam, M.,Tsai, M.D.,Jain, M.K.
      (1996) Biochemistry 35: 12164
    • Phospholipase A2 Engineering. Structural and Functional Roles of the Highly Conserved Active Site Residue Aspartate-99
      Sekar, K.,Yu, B.Z.,Rogers, J.,Lutton, J.,Liu, X.,Chen, X.,Tsai, M.D.,Jain, M.K.,Sundaralingam, M.
      (1997) Biochemistry 36: 3104
    • Phospholipase A2 Engineering. X-Ray Structural and Functional Evidence for the Interaction of Lysine-56 with Substrates
      Noel, J.P.,Bingman, C.A.,Deng, T.L.,Dupureur, C.M.,Hamilton, K.J.,Jiang, R.T.,Kwak, J.G.,Sekharudu, C.,Sundaralingam, M.,Tsai, M.D.
      (1991) Biochemistry 30: 11801
    • Crystal Structure of the Complex of Bovine Pancreatic Phospholipase A2 with a Transition State Analogue
      Sekar, K.,Kumar, A.,Liu, X.,Tsai, M.-D.,Gelb, M.H.,Sundaralingam, M.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Biological Macromolecular Structure Center, Departments of Chemistry and Biochemistry and the Ohio State Biochemistry Program, 100 West 18th Avenue, The Ohio State University, Columbus, OH 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
123Bos taurusMutation(s): 0 
Gene Names: PLA2G1B
EC: 3.1.1.4
Find proteins for P00593 (Bos taurus)
Go to Gene View: PLA2G1B
Go to UniProtKB:  P00593
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 46.780α = 90.00
b = 46.780β = 90.00
c = 102.890γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
R-AXISdata collection
R-AXISdata reduction
R-AXISdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-09-06 
  • Released Date: 1998-03-11 
  • Deposition Author(s): Sundaralingam, M.

Revision History 

  • Version 1.0: 1998-03-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection, Other
  • Version 1.4: 2018-04-11
    Type: Data collection