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- PDB-7yu2: Structure of 6-aminohexanoate-oligomer hydrolase NylC, D122G/H130... -

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Basic information

Entry
Database: PDB / ID: 7yu2
TitleStructure of 6-aminohexanoate-oligomer hydrolase NylC, D122G/H130Y/T267C mutant, hydroxylamine-treated
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: 1.21 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 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / entity / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site / _entity.details / _pdbx_validate_planes.type
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 / pdbx_validate_planes
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type

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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)74,84113
Polymers73,8172
Non-polymers1,02511
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-57 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.270, 144.022, 128.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-816-

HOH

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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: 36908.266 Da / Num. of mol.: 2 / Mutation: D122G, H130Y, T267C
Source method: isolated from a genetically manipulated source
Details: Authors state that the long gap between the residues is due to the post-translational auto-cleavage of the nascent polypeptide between Asn266 and Thr267.
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.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 194470 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.068 / Net I/σ(I): 26.7
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 9026 / CC1/2: 0.791 / Rrim(I) all: 0.745 / % possible all: 93.2

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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: 1.21→27.145 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.221 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1428 9810 5.05 %
Rwork0.1157 184450 -
all0.117 --
obs-194260 99.166 %
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: 16.963 Å2
Baniso -1Baniso -2Baniso -3
1-1.547 Å20 Å20 Å2
2---1.275 Å20 Å2
3----0.272 Å2
Refinement stepCycle: LAST / Resolution: 1.21→27.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 63 627 5567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0135434
X-RAY DIFFRACTIONr_bond_other_d0.0030.0155142
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.6437425
X-RAY DIFFRACTIONr_angle_other_deg1.6411.57711813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20520292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74515800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9911557
X-RAY DIFFRACTIONr_chiral_restr0.1240.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026421
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021309
X-RAY DIFFRACTIONr_nbd_refined0.2440.21066
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.24998
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.22659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2443
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1730.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.244
X-RAY DIFFRACTIONr_nbd_other0.2880.2177
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.240
X-RAY DIFFRACTIONr_mcbond_it2.3871.4482840
X-RAY DIFFRACTIONr_mcbond_other2.3871.4482839
X-RAY DIFFRACTIONr_mcangle_it2.812.1783573
X-RAY DIFFRACTIONr_mcangle_other2.8092.1783574
X-RAY DIFFRACTIONr_scbond_it4.5691.8662590
X-RAY DIFFRACTIONr_scbond_other4.441.8472579
X-RAY DIFFRACTIONr_scangle_it4.9822.6873825
X-RAY DIFFRACTIONr_scangle_other4.7822.6523808
X-RAY DIFFRACTIONr_lrange_it5.0119.8375974
X-RAY DIFFRACTIONr_lrange_other5.0119.8455975
X-RAY DIFFRACTIONr_rigid_bond_restr7.498310570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.2430.2666860.23512632X-RAY DIFFRACTION92.9314
1.243-1.2770.2257140.21513145X-RAY DIFFRACTION98.9787
1.277-1.3140.2047300.17512909X-RAY DIFFRACTION100
1.314-1.3550.1656830.14312516X-RAY DIFFRACTION100
1.355-1.3990.1625800.12812266X-RAY DIFFRACTION99.9922
1.399-1.4480.1626440.11811778X-RAY DIFFRACTION99.992
1.448-1.5020.1396140.10311372X-RAY DIFFRACTION99.9917
1.502-1.5640.1396260.09410927X-RAY DIFFRACTION99.9913
1.564-1.6330.1315520.09310555X-RAY DIFFRACTION99.991
1.633-1.7120.1265260.08710073X-RAY DIFFRACTION99.9529
1.712-1.8050.124880.0829635X-RAY DIFFRACTION99.9408
1.805-1.9130.1174880.0829042X-RAY DIFFRACTION99.8533
1.913-2.0450.1184610.0858532X-RAY DIFFRACTION99.756
2.045-2.2080.134420.0977960X-RAY DIFFRACTION99.7744
2.208-2.4170.1253740.0997371X-RAY DIFFRACTION99.7553
2.417-2.6990.1493460.1156695X-RAY DIFFRACTION99.8016
2.699-3.1120.1342930.1145930X-RAY DIFFRACTION99.8075
3.112-3.7990.1322770.1185025X-RAY DIFFRACTION99.512
3.799-5.320.1381860.1233883X-RAY DIFFRACTION96.9271
5.32-27.1450.191000.1892205X-RAY DIFFRACTION92.7565

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