1W7C

PPLO at 1.23 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.112 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.23 A Structure of Pichia Pastoris Lysyl Oxidase Reveals a Lysine-Lysine Cross-Link

Duff, A.P.Cohen, A.E.Ellis, P.J.Hilmer, K.Langley, D.B.Dooley, D.M.Freeman, H.C.Guss, J.M.

(2006) Acta Crystallogr.,Sect.D 62: 1073

  • DOI: 10.1107/S0907444906026333

  • PubMed Abstract: 
  • The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal form has been refined at 1.23 Angstrom resolution. PPLO, a copper amine oxidase (CuAO) with a 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor, differs from most other members ...

    The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal form has been refined at 1.23 Angstrom resolution. PPLO, a copper amine oxidase (CuAO) with a 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor, differs from most other members of the CuAO enzyme family in having the ability to oxidize the side chain of lysine residues in a polypeptide. In the asymmetric unit of the crystals, the structure analysis has located residues 43-779 of the polypeptide chain, seven carbohydrate residues, the active-site Cu atom, an imidazole molecule bound at the active site, two buried Ca(2+) ions, five surface Mg(2+) ions, five surface Cl(-) ions and 1045 water molecules. The crystallographic residuals are R = 0.112 and R(free) = 0.146. The TPQ cofactor and several other active-site residues are poorly ordered, in contrast to the surrounding well ordered structure. A covalent cross-link is observed between two lysine residues, Lys778 and Lys66. The cross-link is likely to have been formed by the oxidation of Lys778 followed by a spontaneous reaction with Lys66. The link is modelled as dehydrolysinonorleucine.


    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSYL OXIDASE
A
747Komagataella pastorisMutation(s): 0 
Gene Names: AOC1
EC: 1.4.3.-
Find proteins for Q96X16 (Komagataella pastoris)
Go to Gene View: AOC1
Go to UniProtKB:  Q96X16
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPQ
Query on TPQ
A
L-PEPTIDE LINKINGC9 H9 N O5TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.112 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.948α = 90.00
b = 67.027β = 118.95
c = 108.688γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-31
    Type: Initial release
  • Version 1.1: 2013-01-16
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-01-30
    Type: Advisory, Data collection, Experimental preparation, Other