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- PDB-7yu0: Structure of 6-aminohexanoate-oligomer hydrolase NylC precursor, ... -

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Basic information

Entry
Database: PDB / ID: 7yu0
TitleStructure of 6-aminohexanoate-oligomer hydrolase NylC precursor, H130Y/N266A/T267A mutant
Components6-aminohexanoate-oligomer endohydrolase
KeywordsHYDROLASE / NYLON OLIGOMER
Function / homology6-aminohexanoate-oligomer endohydrolase / Peptidase S58, DmpA / Peptidase family S58 / nylon catabolic process / ArgJ-like domain superfamily / aminopeptidase activity / 6-aminohexanoate-oligomer endohydrolase
Function and homology information
Biological speciesArthrobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNegoro, S. / Higuchi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)26289317 Japan
CitationJournal: Febs J. / Year: 2023
Title: X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase.
Authors: Negoro, S. / Shibata, N. / Kato, D.I. / Tanaka, Y. / Yasuhira, K. / Nagai, K. / Oshima, S. / Furuno, Y. / Yokoyama, R. / Miyazaki, K. / Takeo, M. / Hengphasatporn, K. / Shigeta, Y. / Lee, Y.H. / Higuchi, Y.
History
DepositionAug 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-aminohexanoate-oligomer endohydrolase
B: 6-aminohexanoate-oligomer endohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,25320
Polymers73,7822
Non-polymers1,47018
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-102 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.242, 144.345, 129.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 6-aminohexanoate-oligomer endohydrolase / 6-aminohexanoate oligomer hydrolase / Ahx endo-type-oligomer hydrolase / Nylon hydrolase / Nylon ...6-aminohexanoate oligomer hydrolase / Ahx endo-type-oligomer hydrolase / Nylon hydrolase / Nylon oligomer-degrading enzyme EIII / Nylonase


Mass: 36891.215 Da / Num. of mol.: 2 / Mutation: H130Y, N266A, T267A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter (bacteria) / Strain: K172 / Gene: nylC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q79F77, 6-aminohexanoate-oligomer endohydrolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 140625 / % possible obs: 98 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Net I/σ(I): 30.4
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 5859 / CC1/2: 0.94 / Rrim(I) all: 0.526 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AXG

3axg


Resolution: 1.35→37.006 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.493 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1394 7049 5.017 %
Rwork0.1106 133463 -
all0.112 --
obs-140512 97.716 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.236 Å2
Baniso -1Baniso -2Baniso -3
1-1.836 Å20 Å20 Å2
2---1.831 Å20 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.35→37.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 88 579 5531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135254
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154947
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.6417177
X-RAY DIFFRACTIONr_angle_other_deg1.4981.57511369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01920.389283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6615766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7171552
X-RAY DIFFRACTIONr_chiral_restr0.0780.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021246
X-RAY DIFFRACTIONr_nbd_refined0.2090.21005
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.24744
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22500
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22420
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2432
X-RAY DIFFRACTIONr_metal_ion_refined0.1590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.228
X-RAY DIFFRACTIONr_nbd_other0.2260.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.232
X-RAY DIFFRACTIONr_mcbond_it1.5811.8972718
X-RAY DIFFRACTIONr_mcbond_other1.5811.8972717
X-RAY DIFFRACTIONr_mcangle_it1.9132.8613408
X-RAY DIFFRACTIONr_mcangle_other1.9132.8613409
X-RAY DIFFRACTIONr_scbond_it2.6542.3472535
X-RAY DIFFRACTIONr_scbond_other2.3962.3112516
X-RAY DIFFRACTIONr_scangle_it3.0193.3913740
X-RAY DIFFRACTIONr_scangle_other2.7823.3363711
X-RAY DIFFRACTIONr_lrange_it3.49325.1015787
X-RAY DIFFRACTIONr_lrange_other3.49325.1095788
X-RAY DIFFRACTIONr_rigid_bond_restr1.706310200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3840.2144470.1938360X-RAY DIFFRACTION83.1555
1.384-1.4220.2124630.1798976X-RAY DIFFRACTION92.2228
1.422-1.4630.1745210.159376X-RAY DIFFRACTION98.5659
1.463-1.5080.1574950.1249148X-RAY DIFFRACTION99.8137
1.508-1.5580.1394280.1078991X-RAY DIFFRACTION99.6931
1.558-1.6120.1464580.0958642X-RAY DIFFRACTION99.6605
1.612-1.6730.1384350.0928382X-RAY DIFFRACTION99.6609
1.673-1.7410.1344010.0867994X-RAY DIFFRACTION99.5612
1.741-1.8190.1313970.0867723X-RAY DIFFRACTION99.6441
1.819-1.9070.124190.0847367X-RAY DIFFRACTION99.5525
1.907-2.010.1153610.0837002X-RAY DIFFRACTION99.4462
2.01-2.1320.1223320.0866663X-RAY DIFFRACTION99.5588
2.132-2.2790.1143310.0846267X-RAY DIFFRACTION99.6978
2.279-2.4620.1133300.0935827X-RAY DIFFRACTION99.6924
2.462-2.6960.1412960.1035401X-RAY DIFFRACTION99.8598
2.696-3.0140.1352620.1114894X-RAY DIFFRACTION99.9031
3.014-3.4790.1282270.1154370X-RAY DIFFRACTION99.8046
3.479-4.2590.1271910.1163678X-RAY DIFFRACTION99.3325
4.259-6.0130.1581510.1422854X-RAY DIFFRACTION98.1064
6.013-37.0060.2441040.2061548X-RAY DIFFRACTION92.4972

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