7CW1 | pdb_00007cw1

Crystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).

PDB DOI: https://doi.org/10.2210/pdb7CW1/pdb

Classification: HYDROLASE
Organism(s): Moesziomyces antarcticus
Mutation(s): No

Deposited: 2020-08-27 Released: 2020-09-16
Deposition Author(s): Suzuki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.191 (Depositor), 0.201 (DCC)
R-Value Work:
0.156 (Depositor), 0.170 (DCC)
R-Value Observed:
0.158 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).

Suzuki, K.

To be published.

Macromolecule Content

Total Structure Weight: 41.05 kDa
Atom Count: 3,218
Modeled Residue Count: 394
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cutinase-like enzyme	A, B	198	Moesziomyces antarcticus	Mutation(s): 0
UniProt
Find proteins for S6BC01 (Pseudozyma antarctica) Explore S6BC01 Go to UniProtKB: S6BC01
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S6BC01
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAD (Subject of Investigation/LOI) Query on CAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	CACODYLIC ACID C₂ H₇ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.191 (Depositor), 0.201 (DCC)
R-Value Work: 0.156 (Depositor), 0.170 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.065	α = 90
b = 61.587	β = 90
c = 110.387	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
CRANK2	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.