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

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Basic information

Entry
Database: PDB / ID: 9cxr
TitleX-ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 at Room Temperature
ComponentsPoly(hexamethylene adipamide) hydrolase
KeywordsHYDROLASE / NYLON OLIGOMER
Function / homologyPeptidase S58, DmpA / Peptidase family S58 / ArgJ-like domain superfamily / aminopeptidase activity / TRIETHYLENE GLYCOL / Peptidase S58 family protein
Function and homology information
Biological speciesAlphaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMeilleur, F. / Williams, A.N. / Drufva, E.E. / Parks, J.M. / Chen, S.H. / Michener, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) 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
DepositionJul 31, 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
AA: Poly(hexamethylene adipamide) hydrolase
BA: Poly(hexamethylene adipamide) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1268
Polymers62,8222
Non-polymers3046
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-62 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.014, 96.643, 105.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11AA-611-

HOH

21BA-588-

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.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: batch mode
Details: Hampton Research PEGRx HT-D2 (Imidazole 0.1 M, Polyethylene glycol 6,000 20.0 w/v)

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Data collection

DiffractionMean temperature: 293 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: Mar 26, 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: 2.2→25.38 Å / Num. obs: 28405 / % possible obs: 98.63 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.42 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.1775 / Rpim(I) all: 0.093 / Rrim(I) all: 0.2012 / Net I/σ(I): 9.98
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.5051 / Num. unique obs: 2797 / CC1/2: 0.798 / Rpim(I) all: 0.263 / Rrim(I) all: 0.5717 / % possible all: 99.47

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25.38 Å / SU ML: 0.2093 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 1307 4.62 %
Rwork0.1582 27010 -
obs0.1605 28317 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 18 204 4570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234532
X-RAY DIFFRACTIONf_angle_d0.49156157
X-RAY DIFFRACTIONf_chiral_restr0.042723
X-RAY DIFFRACTIONf_plane_restr0.0033813
X-RAY DIFFRACTIONf_dihedral_angle_d15.48041637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.2511460.17592961X-RAY DIFFRACTION99.39
2.29-2.390.29141510.18662946X-RAY DIFFRACTION98.66
2.39-2.520.26351680.19192946X-RAY DIFFRACTION99.08
2.52-2.680.29681260.18382976X-RAY DIFFRACTION98.73
2.68-2.880.21611270.17363015X-RAY DIFFRACTION99.3
2.88-3.170.20591400.16523012X-RAY DIFFRACTION99.03
3.17-3.630.18861530.14133000X-RAY DIFFRACTION99.18
3.63-4.570.14561490.11493052X-RAY DIFFRACTION99.04
4.57-25.380.16281470.15993102X-RAY DIFFRACTION96.24

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