9Z2I | pdb_00009z2i

Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 in its Apo form at Room Temperature

PDB DOI: https://doi.org/10.2210/pdb9Z2I/pdb

Classification: HYDROLASE
Organism(s): Alphaproteobacteria bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-11-05 Released: 2025-11-19
Deposition Author(s): Capra, N., Meilleur, F.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.196 (Depositor), 0.190 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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Literature

Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 at Room Temperature in the Apo form

Capra, N., Meilleur, F.

To be published.

Macromolecule Content

Total Structure Weight: 62.87 kDa
Atom Count: 4,544
Modeled Residue Count: 605
Deposited Residue Count: 610
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(hexamethylene adipamide) hydrolase	A, B	305	Alphaproteobacteria bacterium	Mutation(s): 0 Gene Names: EPN97_01225 EC: 3.5.1.117

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.20 Å
R-Value Free: 0.196 (Depositor), 0.190 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.755	α = 90
b = 96.398	β = 90
c = 104.618	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
CrysalisPro	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release
Version 1.1: 2025-11-26
Changes: Author supporting evidence

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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.