9L75 | pdb_00009l75

A novel PE hydrolase and its structural basis

PDB DOI: https://doi.org/10.2210/pdb9L75/pdb

Classification: HYDROLASE
Organism(s): Vreelandella venusta
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-25 Released: 2025-12-31
Deposition Author(s): Wang, Y.S., Sun, D.Y., Jia, H.H., Sun, Y.Z., Qiu, L.N.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.263 (Depositor), 0.269 (DCC)
R-Value Work:
0.206 (Depositor), 0.216 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

A novel PE hydrolase and its structural basis

Wang, Y.S., Sun, D.Y., Jia, H.H., Sun, Y.Z., Qiu, L.N.

To be published.

Macromolecule Content

Total Structure Weight: 63.11 kDa
Atom Count: 4,362
Modeled Residue Count: 542
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase	A, B	281	Vreelandella venusta	Mutation(s): 0 Gene Names: JDS37_04195
UniProt
Find proteins for A0AAQ0CHA8 (Vreelandella venusta) Explore A0AAQ0CHA8 Go to UniProtKB: A0AAQ0CHA8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAQ0CHA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.263 (Depositor), 0.269 (DCC)
R-Value Work: 0.206 (Depositor), 0.216 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.42	α = 90
b = 169.42	β = 90
c = 54.99	γ = 120

Software Package:

Software Name	Purpose
AMBER	refinement
AMBER	refinement
APEX 2	data reduction
APEX 2	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	--

Revision History (Full details and data files)

Version 1.0: 2025-12-31
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.