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- PDB-9dys: X-ray Crystallographic Structure of the Poly(Hexamethylene Adipam... -

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Basic information

Entry
Database: PDB / ID: 9dys
TitleX-ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 at Room Temperature bound to tetraethylene glycol
ComponentsPoly(hexamethylene adipamide) hydrolase
KeywordsHYDROLASE / Nylon hydrolase / Nylon66 / nylon hydrolysis / thermostable
Function / homologyPeptidase S58, DmpA / Peptidase family S58 / ArgJ-like domain superfamily / aminopeptidase activity / Peptidase S58 family protein
Function and homology information
Biological speciesAlphaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsCapra, N. / Meilleur, F.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC05-00OR22725 United States
CitationJournal: Biorxiv / Year: 2024
Title: Identification and characterization of substrate- and product-selective nylon hydrolases.
Authors: Drufva, E.E. / Cahill, J.F. / Saint-Vincent, P.M.B. / Williams, A.N. / Bocharova, V. / Capra, N. / Meilleur, F. / Carper, D.L. / Bourgery, C. / Miyazaki, K. / Yonemura, M. / Shiraishi, Y. / ...Authors: Drufva, E.E. / Cahill, J.F. / Saint-Vincent, P.M.B. / Williams, A.N. / Bocharova, V. / Capra, N. / Meilleur, F. / Carper, D.L. / Bourgery, C. / Miyazaki, K. / Yonemura, M. / Shiraishi, Y. / Parks, J.M. / Zhou, M. / Dishner, I.T. / Foster, J.C. / Koehler, S.J. / Valentino, H.R. / Sedova, A. / Kertesz, V. / Vasileva, D.P. / Hochanadel, L.H. / Figg, C.A. / Negoro, S. / Kato, D.I. / Chen, S.H. / Michener, J.K.
History
DepositionOct 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: 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)63,1246
Polymers62,8222
Non-polymers3024
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-39 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.879, 96.511, 105.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-602-

HOH

31B-600-

HOH

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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: UniProt: A0A522DD61
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.18 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.9
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: Oct 4, 2024 / Details: Osmic VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→26.73 Å / Num. obs: 47261 / % possible obs: 99.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.038 / Rrim(I) all: 0.105 / Χ2: 0.92 / Net I/σ(I): 11.9
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 90.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.662 / Num. measured all: 11136 / Num. unique obs: 2605 / CC1/2: 0.703 / Rpim(I) all: 0.34 / Rrim(I) all: 0.751 / Χ2: 1.18 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
CrysalisProdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→26.73 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.346 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17219 2470 5.2 %RANDOM
Rwork0.15057 ---
obs0.1517 44737 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.85→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 19 203 4570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124458
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164357
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.7966036
X-RAY DIFFRACTIONr_angle_other_deg0.5911.7319996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.452536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75610703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
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_it2.1111.942427
X-RAY DIFFRACTIONr_mcbond_other2.1041.942427
X-RAY DIFFRACTIONr_mcangle_it2.9633.4733030
X-RAY DIFFRACTIONr_mcangle_other2.9633.4743031
X-RAY DIFFRACTIONr_scbond_it4.1032.5612031
X-RAY DIFFRACTIONr_scbond_other4.1032.5632032
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2454.4023004
X-RAY DIFFRACTIONr_long_range_B_refined7.54719.544624
X-RAY DIFFRACTIONr_long_range_B_other7.52819.284608
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 159 -
Rwork0.238 2966 -
obs--91.19 %

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