7CY9 | pdb_00007cy9

Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9 solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).

• PDB DOI: https://doi.org/10.2210/pdb7CY9/pdb

• Classification: HYDROLASE
• Organism(s): Paraphoma sp. B47-9
• Mutation(s): No 


• Deposited: 2020-09-03 Released: 2020-09-30 
• Deposition Author(s): Suzuki, K., Koitabashi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.166 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Literature

Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9 solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).

Suzuki, K., Koitabashi, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.41 kDa 
• Atom Count: 3,158 
• Modeled Residue Count: 387 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cutinase	A, B	195	Paraphoma sp. B47-9	Mutation(s): 0  EC: 3.1.1.74
UniProt
Find proteins for A0A060N399 (Paraphoma sp. B47-9) Explore A0A060N399  Go to UniProtKB:  A0A060N399

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAD (Subject of Investigation/LOI)	C [auth A], D [auth A], G [auth B]	CACODYLIC ACID C2 H7 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-N
NA	E [auth A], F [auth A], H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.166 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.886	α = 103.78
b = 43.517	β = 92.42
c = 51.724	γ = 101.49

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
SHELX	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Suzuki, K., Koitabashi, M.

Revision History  

• 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, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary