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- PDB-9z0b: Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexame... -

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Basic information

Entry
Database: PDB / ID: 9z0b
TitleCrystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Cryo Temperature
ComponentsPoly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
KeywordsHYDROLASE / Nylon hydrolase / amidase / Ntn-hydrolase / amide bond hydrolase
Function / homologyACETATE ION / CHOLINE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesGammaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
B: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
C: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
D: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
E: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
F: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
G: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
H: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,99422
Polymers281,1518
Non-polymers1,84214
Water14,970831
1
A: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
F: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
H: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
hetero molecules

G: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,37910
Polymers140,5764
Non-polymers8036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Buried area22200 Å2
ΔGint-93 kcal/mol
Surface area36810 Å2
MethodPISA
2
C: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
D: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
hetero molecules

B: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
E: Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,61512
Polymers140,5764
Non-polymers1,0398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-3/2,-y,z+1/21
Buried area21550 Å2
ΔGint-92 kcal/mol
Surface area36390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.623, 135.407, 142.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12


Mass: 35143.918 Da / Num. of mol.: 8
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

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Non-polymers , 7 types, 845 molecules

#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.33 % / Description: Large, irregular, three-dimensional crystal
Crystal growTemperature: 291 K / Method: liquid diffusion / pH: 7.4
Details: 0.09 M HEPES, pH 6.8, 27% w/v PEG3350, 5% v/v cholin acetate (HR Ionic Liquid 5), protein:ML ratio of 2:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→98.28 Å / Num. obs: 217968 / % possible obs: 93.7 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.055 / Rrim(I) all: 0.145 / Χ2: 0.84 / Net I/σ(I): 8.2
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 98 % / Redundancy: 6.4 % / Rmerge(I) obs: 1.177 / Num. measured all: 71568 / Num. unique obs: 11205 / CC1/2: 0.646 / Rpim(I) all: 0.497 / Rrim(I) all: 1.28 / Χ2: 0.73 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→98.28 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.568 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19653 10809 5 %RANDOM
Rwork0.16117 ---
obs0.16293 207043 93.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.645 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å20 Å2
2---0.04 Å20 Å2
3---1.08 Å2
Refinement stepCycle: 1 / Resolution: 1.75→98.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18743 0 119 831 19693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01219242
X-RAY DIFFRACTIONr_bond_other_d0.0010.01618644
X-RAY DIFFRACTIONr_angle_refined_deg2.2251.79126068
X-RAY DIFFRACTIONr_angle_other_deg0.891.73142832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85752467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.223562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.149103097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1810.22969
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222486
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024346
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_it3.051.9189927
X-RAY DIFFRACTIONr_mcbond_other3.0431.9179925
X-RAY DIFFRACTIONr_mcangle_it3.9423.40812373
X-RAY DIFFRACTIONr_mcangle_other3.9433.40812374
X-RAY DIFFRACTIONr_scbond_it5.2472.5069315
X-RAY DIFFRACTIONr_scbond_other5.2372.5059312
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4094.33913690
X-RAY DIFFRACTIONr_long_range_B_refined7.82625.9981150
X-RAY DIFFRACTIONr_long_range_B_other7.82725.980611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 784 -
Rwork0.248 15873 -
obs--97.53 %

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