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- PDB-9z0a: Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexame... -

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Entry
Database: PDB / ID: 9z0a
TitleCrystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Room Temperature
ComponentsPolycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12
KeywordsHYDROLASE / Nylon hydrolase / Ntn-hydrolase / Generalist hydrolase / Nylon-6 / Nylon-66
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesGammaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCapra, N. / Meilleur, F.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Biorxiv / Year: 2026
Title: Structural and oligomeric characterization of substrate- and product-selective nylon hydrolases.
Authors: Capra, N. / Bourgery, C. / Parks, J.M. / Carper, D.L. / Cahill, J.F. / Michener, J.K. / Meilleur, F.
History
DepositionOct 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12
B: Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5444
Polymers70,2882
Non-polymers2562
Water3,279182
1
A: Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12
B: Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12
hetero molecules

A: Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12
B: Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0888
Polymers140,5764
Non-polymers5134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area22300 Å2
ΔGint-115 kcal/mol
Surface area36240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.593, 79.428, 108.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12


Mass: 35143.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gammaproteobacteria bacterium (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: 6-aminohexanoate-oligomer endohydrolase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.5 % / Description: Small, rod-like crystal
Crystal growTemperature: 291 K / Method: microbatch
Details: 0.09 M HEPES, pH 6.8, 27% w/v PEG3350, 5% v/v cholin acetate (HR Ionic Liquid 5), protein:cocktail ratio of 2:1

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541838 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 1, 2025 / Details: Osmic VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541838 Å / Relative weight: 1
ReflectionResolution: 1.9→29.64 Å / Num. obs: 53622 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.069 / Χ2: 0.84 / Net I/σ(I): 13.3 / Num. measured all: 314936
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.637 / Num. measured all: 14308 / Num. unique obs: 3584 / CC1/2: 0.723 / Rpim(I) all: 0.364 / Rrim(I) all: 0.737 / Χ2: 0.98 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.89 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19585 2688 5 %RANDOM
Rwork0.15104 ---
obs0.15327 50888 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0 Å2
2---0.66 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4657 0 17 182 4856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0124780
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164637
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.796462
X-RAY DIFFRACTIONr_angle_other_deg0.8111.7310654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9045611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.264516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49910767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1390.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021083
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.972.6782462
X-RAY DIFFRACTIONr_mcbond_other3.9692.6812463
X-RAY DIFFRACTIONr_mcangle_it5.1274.7543067
X-RAY DIFFRACTIONr_mcangle_other5.1294.7573068
X-RAY DIFFRACTIONr_scbond_it6.3423.452318
X-RAY DIFFRACTIONr_scbond_other6.3413.452319
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.985.993396
X-RAY DIFFRACTIONr_long_range_B_refined9.46233.419344
X-RAY DIFFRACTIONr_long_range_B_other9.46233.4219343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 192 -
Rwork0.266 3694 -
obs--99.85 %

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