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

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Basic information

Entry
Database: PDB / ID: 5xyp
TitleStructure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D122R 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: 1.2 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 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
Revision 1.2Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)74,3406
Polymers73,9632
Non-polymers3774
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)148,67912
Polymers147,9254
Non-polymers7548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area17990 Å2
ΔGint-123 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.251, 145.112, 128.556
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-685-

HOH

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Components

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


Mass: 36981.340 Da / Num. of mol.: 2 / Mutation: D122R
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


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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: 44.47 %
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: 1.2→50 Å / Num. obs: 203670 / % possible obs: 99.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.5
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.97 / % possible all: 98.9

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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: 1.2→45.08 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.831 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14338 9466 5.1 %RANDOM
Rwork0.12185 ---
obs0.12293 177816 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16.312 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.28 Å20 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.2→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 0 21 595 5499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225240
X-RAY DIFFRACTIONr_bond_other_d00.023541
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9577148
X-RAY DIFFRACTIONr_angle_other_deg0.8638560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56322.212226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.50815757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6861555
X-RAY DIFFRACTIONr_chiral_restr0.1040.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021140
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_it3.36323414
X-RAY DIFFRACTIONr_mcbond_other4.01421418
X-RAY DIFFRACTIONr_mcangle_it4.72535453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.5254.51826
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.26461683
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.84135232
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.199→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 380 -
Rwork0.134 6594 -
obs--46.91 %

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