7CY3

Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.127 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9.

Suzuki, K.Koitabashi, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cutinase
A, B
195Paraphoma sp. B47-9Mutation(s): 0 
EC: 3.1.1.74
UniProt
Find proteins for A0A060N399 (Paraphoma sp. B47-9)
Explore A0A060N399 
Go to UniProtKB:  A0A060N399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A060N399
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAD (Subject of Investigation/LOI)
Query on CAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
CACODYLIC ACID
C2 H7 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.127 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.886α = 103.78
b = 43.517β = 92.42
c = 51.724γ = 101.49
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
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: 2020-09-30
    Type: Initial release
  • Version 2.0: 2020-12-16
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary