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

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Basic information

Entry
Database: PDB / ID: 9yys
TitleCrystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl10 at Cryo Temperature
ComponentsL-aminopeptidase/D-esterase
KeywordsHYDROLASE / Nylon hydrolase / amidase / Ntn-hydrolase / amide bond hydrolase
Function / homologyPeptidase S58, DmpA / Peptidase family S58 / ArgJ-like domain superfamily / aminopeptidase activity / D-MALATE / PYRUVIC ACID / L-aminopeptidase/D-esterase
Function and homology information
Biological speciesJatrophihabitans endophyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-aminopeptidase/D-esterase
B: L-aminopeptidase/D-esterase
C: L-aminopeptidase/D-esterase
D: L-aminopeptidase/D-esterase
E: L-aminopeptidase/D-esterase
F: L-aminopeptidase/D-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,17413
Polymers173,4996
Non-polymers6757
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Not concentration dependent 30, 75, 150, 300 uM (1, 2.5, 5, 10 mg/ml), mass spectrometry, 20 nM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.126, 120.193, 148.305
Angle α, β, γ (deg.)90.00, 92.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-aminopeptidase/D-esterase


Mass: 28916.520 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jatrophihabitans endophyticus (bacteria)
Gene: SAMN05443575_2985 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M5P6R3
#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.13 Å3/Da / Density % sol: 42 % / Description: Small, three-dimensional
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.7 / Details: 0.5 M DL-malic acid pH 4.7, 15% w/v PEG 3350

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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: 1.3→74.05 Å / Num. obs: 351281 / % possible obs: 98.8 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.039 / Rrim(I) all: 0.059 / Χ2: 0.93 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
7.12-74.0540.02833.322420.9980.0250.0380.8799.8
1.3-1.323.80.9851.4174490.440.8651.3161.0199.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
autoPROCdata processing
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→68.4 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.666 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17013 17757 5.1 %RANDOM
Rwork0.14247 ---
obs0.14387 333519 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.399 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å2-0 Å21.03 Å2
2---0.28 Å20 Å2
3----2.7 Å2
Refinement stepCycle: 1 / Resolution: 1.3→68.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11558 0 45 775 12378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01211887
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611416
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.78616245
X-RAY DIFFRACTIONr_angle_other_deg0.6221.73626026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6851650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.5325133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.185101616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022635
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_it6.2432.1446609
X-RAY DIFFRACTIONr_mcbond_other6.2142.1436603
X-RAY DIFFRACTIONr_mcangle_it8.2783.8578255
X-RAY DIFFRACTIONr_mcangle_other8.2673.8578253
X-RAY DIFFRACTIONr_scbond_it8.2372.4845278
X-RAY DIFFRACTIONr_scbond_other8.2362.4845279
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.1594.4247991
X-RAY DIFFRACTIONr_long_range_B_refined15.55126.7651856
X-RAY DIFFRACTIONr_long_range_B_other13.88726.6351261
X-RAY DIFFRACTIONr_rigid_bond_restr5.199323303
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 1350 -
Rwork0.265 24696 -
obs--99.2 %

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