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- PDB-9z11: Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) ... -

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Basic information

Entry
Database: PDB / ID: 9z11
TitleCrystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 in Complex with Butyrate at Room Temperature
ComponentsPoly (Hexamethylene adipamide) hydrolase
KeywordsHYDROLASE / Nylon hydrolase / Ntn-hydrolase / Nylon-66
Function / homologybutanoic acid
Function and homology information
Biological speciesAlphaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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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)62,9984
Polymers62,8222
Non-polymers1762
Water1,27971
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)125,9968
Polymers125,6444
Non-polymers3524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_565x,-y+1,-z1
Buried area15150 Å2
ΔGint-42 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.881, 96.478, 105.464
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)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: EC: 3.5.117
#2: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.7 % / 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: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→28.41 Å / Num. obs: 36372 / % possible obs: 96.9 % / Redundancy: 6.4 % / CC1/2: 0.968 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Χ2: 0.9 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.05 Å / % possible obs: 95.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.555 / Num. measured all: 14808 / Num. unique obs: 2307 / CC1/2: 0.9 / Rpim(I) all: 0.234 / Rrim(I) all: 0.604 / Χ2: 1.03 / Net I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.41 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.572 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21688 1863 5.1 %RANDOM
Rwork0.16798 ---
obs0.17046 34463 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å20 Å2
2---0.22 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 2→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 12 71 4389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124387
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164270
X-RAY DIFFRACTIONr_angle_refined_deg2.3381.7955951
X-RAY DIFFRACTIONr_angle_other_deg0.7471.7319791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.038534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39410685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025261
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02947
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_it3.8092.7712403
X-RAY DIFFRACTIONr_mcbond_other3.8022.7722403
X-RAY DIFFRACTIONr_mcangle_it4.8934.9632999
X-RAY DIFFRACTIONr_mcangle_other4.8944.9653000
X-RAY DIFFRACTIONr_scbond_it5.6743.3991984
X-RAY DIFFRACTIONr_scbond_other5.6663.3981983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9035.9342952
X-RAY DIFFRACTIONr_long_range_B_refined8.94527.324466
X-RAY DIFFRACTIONr_long_range_B_other8.94227.324465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 131 -
Rwork0.278 2430 -
obs--94.29 %

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