9K0H | pdb_00009k0h

The Crystal Structure of dsPETase05 from Biortus

PDB DOI: https://doi.org/10.2210/pdb9K0H/pdb

Classification: HYDROLASE
Organism(s): Pseudomonadota bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-15 Released: 2025-10-22
Deposition Author(s): Wan, T., Wang, F., Lv, Z., Lin, D., Pan, W., Shang, H., Sun, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.195 (Depositor), 0.208 (DCC)
R-Value Work:
0.148 (Depositor), 0.160 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

The Crystal Structure of dsPETase05 from Biortus

Wan, T., Wang, F., Lv, Z., Lin, D., Pan, W., Shang, H., Sun, J.

To be published.

Macromolecule Content

Total Structure Weight: 55.64 kDa
Atom Count: 4,378
Modeled Residue Count: 514
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase	A, B	268	Pseudomonadota bacterium	Mutation(s): 0
UniProt
Find proteins for A0A1S8DDV9 (Halopseudomonas pachastrellae) Explore A0A1S8DDV9 Go to UniProtKB: A0A1S8DDV9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1S8DDV9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.195 (Depositor), 0.208 (DCC)
R-Value Work: 0.148 (Depositor), 0.160 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.066	α = 90
b = 67.273	β = 96.529
c = 85.446	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MoRDa	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

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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.