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

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Basic information

Entry
Database: PDB / ID: 5xyo
TitleStructure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D122G 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 / MOLECULAR REPLACEMENT / Resolution: 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 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)74,1187
Polymers73,7622
Non-polymers3555
Water5,711317
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)148,23514
Polymers147,5254
Non-polymers71010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area17720 Å2
ΔGint-169 kcal/mol
Surface area40010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.485, 144.459, 128.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
22B

NCS domain segments:

End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYAA15 - 35515 - 355
222ASPASPBB19 - 35519 - 355

NCS ensembles :
ID
2
1

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Components

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


Mass: 36881.199 Da / Num. of mol.: 2 / Mutation: D122G
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 44.46 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 43634 / % possible obs: 97.8 % / Redundancy: 2.79 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.2 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XYG

5xyg


Resolution: 2→72.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.057 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.22585 2200 5 %RANDOM
Rwork0.17317 ---
obs0.17585 41403 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 27.022 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å2-0 Å2
2---1.66 Å20 Å2
3----1.54 Å2
Refinement stepCycle: 1 / Resolution: 2→72.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 18 317 5196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9566834
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8565668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6322.651215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17615715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5141547
X-RAY DIFFRACTIONr_chiral_restr0.0950.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213932
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_it2.28523284
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.25835230
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2514.51735
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9661598
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1308medium positional0.220.5
1077loose positional0.535
1308medium thermal2.082
1077loose thermal310
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 122 -
Rwork0.264 2542 -
obs--81.79 %
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)
10.2125-0.082-0.01430.2150.08690.3183-0.0028-0.0035-0.0022-0.03520.0009-0.0024-0.03660.00070.00190.00970.00440.00160.0238-0.00340.0248-1.1026-30.539316.1286
20.1467-0.0539-0.01280.2803-0.04550.21290.00020.00610.0027-0.04440.01840.02660.038-0.022-0.01860.0128-0.003-0.00990.02540.00280.0226-7.5507-63.254118.0947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 355
2X-RAY DIFFRACTION2B1 - 355

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