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- PDB-5y0l: Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacte... -

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Basic information

Entry
Database: PDB / ID: 5y0l
TitleStructure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D122G/H130Y 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
6-aminohexanoate-oligomer endohydrolase / 6-aminohexanoate-oligomer endohydrolase
Similarity search - Component
Biological speciesFlavobacterium sp. KI723T1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.385 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)74,1397
Polymers73,8122
Non-polymers3265
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-43 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.880, 144.003, 129.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-722-

HOH

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Components

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


Mass: 36906.227 Da / Num. of mol.: 2 / Mutation: D122G, H130Y
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
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: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.385→100 Å / Num. obs: 128858 / % possible obs: 99.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 38.5
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.886 / Num. unique obs: 6285 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XYG

5xyg


Resolution: 1.385→72 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.875 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19952 6406 5.1 %RANDOM
Rwork0.17128 ---
obs0.17269 120263 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.563 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å2-0 Å2
2---1.64 Å20 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 1.385→72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 19 632 5541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9587137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25622.489225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27615759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6061552
X-RAY DIFFRACTIONr_chiral_restr0.1250.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214126
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.91723410
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7735450
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.394.51818
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.25161670
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.385→1.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 367 -
Rwork0.296 7003 -
obs--76.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2466-0.13930.13150.63-0.1790.63050.01820.0134-0.0163-0.05850.01570.06540.0333-0.0597-0.0340.0081-0.0065-0.00490.0392-0.00420.053597.451-62.78147.089
20.4251-0.0678-0.05890.54730.1710.6214-0.00390.0110.019-0.05260.0053-0.0228-0.04440.0113-0.00130.00740.00380.0020.04350.00560.0475103.414-30.208145.676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 355
2X-RAY DIFFRACTION2B15 - 355

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