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- PDB-9z0z: Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) ... -

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Basic information

Entry
Database: PDB / ID: 9z0z
TitleCrystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 Acylenzyme Complex at Room Temperature
ComponentsPoly(hexamethylene adipamide) hydrolase
KeywordsHYDROLASE / Nylon hydrolase / Ntn-hydrolase / Nylon-66 / acylenzyme
Function / homology:
Function and homology information
Biological speciesAlphaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionNov 3, 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: Poly(hexamethylene adipamide) hydrolase
B: Poly(hexamethylene adipamide) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3566
Polymers62,8222
Non-polymers5354
Water00
1
A: Poly(hexamethylene adipamide) hydrolase
B: Poly(hexamethylene adipamide) hydrolase
hetero molecules

A: Poly(hexamethylene adipamide) hydrolase
B: Poly(hexamethylene adipamide) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,71312
Polymers125,6444
Non-polymers1,0698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area14820 Å2
ΔGint-115 kcal/mol
Surface area34670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.810, 96.446, 104.663
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 Poly(hexamethylene adipamide) hydrolase


Mass: 31410.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alphaproteobacteria bacterium (bacteria)
Gene: EPN97_01225 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: 6-aminohexanoate-oligomer endohydrolase
#2: Chemical ChemComp-A1CZU / N-(6-aminohexyl)-6-oxohexanamide


Mass: 244.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.4 % / Description: Small, rod-like crystal
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.4
Details: Imidazole 0.1 M pH 6.9, Polyethylene glycol 6,000 20.0% w/v

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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: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541838 Å / Relative weight: 1
ReflectionResolution: 3.1→27.39 Å / Num. obs: 10389 / % possible obs: 99.8 % / Redundancy: 9.5 % / CC1/2: 0.983 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.089 / Rrim(I) all: 0.28 / Χ2: 0.74 / Net I/σ(I): 9.9 / Num. measured all: 98455
Reflection shellResolution: 3.1→3.31 Å / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.587 / Num. measured all: 17990 / Num. unique obs: 1842 / CC1/2: 0.903 / Rpim(I) all: 0.195 / Rrim(I) all: 0.619 / Χ2: 0.57 / Net I/σ(I) obs: 4.5

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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: 3.1→27.39 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.897 / SU B: 18.408 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21843 528 5.1 %RANDOM
Rwork0.14283 ---
obs0.14676 9831 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2--0.15 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 3.1→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 34 0 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124467
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164366
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.7996047
X-RAY DIFFRACTIONr_angle_other_deg0.6041.74110017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5825610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.337536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40310703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02967
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_it1.4360.6912433
X-RAY DIFFRACTIONr_mcbond_other1.4360.6912431
X-RAY DIFFRACTIONr_mcangle_it2.2621.2323035
X-RAY DIFFRACTIONr_mcangle_other2.2611.2323036
X-RAY DIFFRACTIONr_scbond_it2.1590.9062034
X-RAY DIFFRACTIONr_scbond_other2.1590.9072035
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4731.5413010
X-RAY DIFFRACTIONr_long_range_B_refined6.0547.5918355
X-RAY DIFFRACTIONr_long_range_B_other6.0547.5918356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 28 -
Rwork0.181 730 -
obs--99.87 %

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