1PLU

PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).

Yoder, M.D.Jurnak, F.

(1995) Plant Physiol 107: 349-364

  • DOI: 10.1104/pp.107.2.349
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of pectate lyase C (EC 4.2.2.2) from the enterobacterium Erwinia chrysanthemi (PelC) has been refined by molecular dynamics techniques to a resolution of 2.2 A to an R factor of 17.97%. The final model consists of 352 of the tot ...

    The crystal structure of pectate lyase C (EC 4.2.2.2) from the enterobacterium Erwinia chrysanthemi (PelC) has been refined by molecular dynamics techniques to a resolution of 2.2 A to an R factor of 17.97%. The final model consists of 352 of the total 353 amino acids and 114 solvent molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.768[deg] for bond angles. The structure of PelC bound to the lanthanide ion lutetium, used as a calcium analog, has also been refined. Lutetium inhibits the enzymatic activity of the protein, and in the PelC-lutetium structure, the ion binds in the putative calcium-binding site. Five side-chain atoms form ligands to the lutetium ion. An analysis of the atomic-level model of the two protein structures reveals possible implications for the enzymatic mechanism of the enzyme.


    Organizational Affiliation

    School of Biological Sciences, Division of Cell Biology and Biophysics, University of Missouri, Kansas City, Missouri 64110 (M.D.Y.).



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PECTATE LYASE C)A353Dickeya chrysanthemiMutation(s): 0 
Gene Names: pelC
EC: 4.2.2.2
Find proteins for P11073 (Dickeya chrysanthemi)
Explore P11073 
Go to UniProtKB:  P11073
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LU
Query on LU

Download CCD File 
A
LUTETIUM (III) ION
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.6α = 90
b = 80.6β = 90
c = 95.7γ = 90
Software Package:
Software NamePurpose
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
X-PLORrefinement
SDMSdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description