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

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Basic information

Entry
Database: PDB / ID: 5xyq
TitleStructure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D122K mutant
ComponentsEndo-type 6-aminohexanoate oligomer hydrolase
KeywordsHYDROLASE / Nylon oligomer
Function / homology
Function and homology information


6-aminohexanoate-oligomer endohydrolase / nylon catabolic process / hydrolase 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: 1.1 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 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)74,4658
Polymers73,9072
Non-polymers5586
Water12,052669
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)148,93016
Polymers147,8134
Non-polymers1,11712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area20110 Å2
ΔGint-135 kcal/mol
Surface area38510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.660, 144.783, 128.194
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-639-

HOH

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Components

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


Mass: 36953.328 Da / Num. of mol.: 2 / Mutation: D122K
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
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: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 264009 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.2
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.12 / % possible all: 99.5

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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: 1.1→39.85 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.714 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1427 11697 5 %RANDOM
Rwork0.12243 ---
obs0.12344 220658 87.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 17.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0 Å2
2---0.12 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.1→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4879 0 34 669 5582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225327
X-RAY DIFFRACTIONr_bond_other_d00.023589
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9627269
X-RAY DIFFRACTIONr_angle_other_deg0.85438707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81422.727231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34815779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0551552
X-RAY DIFFRACTIONr_chiral_restr0.10.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021134
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_it3.08523472
X-RAY DIFFRACTIONr_mcbond_other4.10721439
X-RAY DIFFRACTIONr_mcangle_it4.41635553
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.864.51855
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.41361702
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.55335310
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 204 -
Rwork0.187 3857 -
obs--21.06 %

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