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- PDB-5y0m: Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacte... -

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Basic information

Entry
Database: PDB / ID: 5y0m
TitleStructure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q mutant
ComponentsEndo-type 6-aminohexanoate oligomer hydrolase
KeywordsHYDROLASE / Nylon oligomer
Function / homology
Function and homology information


6-aminohexanoate-oligomer endohydrolase / nylon catabolic process / aminopeptidase activity
Similarity search - Function
Peptidase S58, DmpA / Peptidase family S58 / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 6-aminohexanoate-oligomer endohydrolase / 6-aminohexanoate-oligomer endohydrolase
Similarity search - Component
Biological speciesFlavobacterium sp. KI723T1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsNegoro, S. / Shibata, N. / Nagai, K. / Higuchi, Y.
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase
Authors: Negoro, S. / Shibata, N. / Lee, Y.H. / Takehara, I. / Kinugasa, R. / Nagai, K. / Tanaka, Y. / Kato, D.I. / Takeo, M. / Goto, Y. / Higuchi, Y.
History
DepositionJul 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 15, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-type 6-aminohexanoate oligomer hydrolase
B: Endo-type 6-aminohexanoate oligomer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,15920
Polymers73,7222
Non-polymers1,43718
Water10,719595
1
A: Endo-type 6-aminohexanoate oligomer hydrolase
B: Endo-type 6-aminohexanoate oligomer hydrolase
hetero molecules

A: Endo-type 6-aminohexanoate oligomer hydrolase
B: Endo-type 6-aminohexanoate oligomer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,31940
Polymers147,4454
Non-polymers2,87436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area25940 Å2
ΔGint-217 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.418, 144.424, 128.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Endo-type 6-aminohexanoate oligomer hydrolase


Mass: 36861.234 Da / Num. of mol.: 2 / Fragment: D36A, D122G, H130Y, E263Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. KI723T1 (bacteria) / Gene: nylC / Production host: Escherichia coli (E. coli) / References: UniProt: Q57326, UniProt: Q79F77*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the long gap between the residues is due to the post-translational auto-cleavage ...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.

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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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2-2.2 M ammonium sulphate, 0.2 M NaCl, 0.1 M HEPES buffer pH 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.03→100 Å / Num. obs: 318913 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.9
Reflection shellResolution: 1.03→1.04 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 12557 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→72.21 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.503 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13442 16076 5 %RANDOM
Rwork0.11602 ---
obs0.11693 302599 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 10.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.19 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.03→72.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4844 0 86 595 5525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225570
X-RAY DIFFRACTIONr_bond_other_d0.0010.023840
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9677631
X-RAY DIFFRACTIONr_angle_other_deg1.07539317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45122.181243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3815837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2761561
X-RAY DIFFRACTIONr_chiral_restr0.120.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216487
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021220
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_it2.91923546
X-RAY DIFFRACTIONr_mcbond_other4.17721471
X-RAY DIFFRACTIONr_mcangle_it4.10835709
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.6724.52024
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.75761875
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.39335559
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 1098 -
Rwork0.216 22025 -
obs--98.73 %

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