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- PDB-3a2p: Structure of 6-aminohexanoate cyclic dimer hydrolase -

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Basic information

Entry
Database: PDB / ID: 3a2p
TitleStructure of 6-aminohexanoate cyclic dimer hydrolase
Components6-aminohexanoate-cyclic-dimer hydrolase
KeywordsHYDROLASE / alpha/beta fold / Nylon degradation
Function / homology
Function and homology information


6-aminohexanoate-cyclic-dimer hydrolase / 6-aminohexanoate-cyclic-dimer hydrolase activity / nylon catabolic process
Similarity search - Function
Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
6-aminohexanoate-cyclic-dimer hydrolase
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsShibata, N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation
Authors: Yasuhira, K. / Shibata, N. / Mongami, G. / Uedo, Y. / Atsumi, Y. / Kawashima, Y. / Hibino, A. / Tanaka, Y. / Lee, Y.-H. / Kato, D. / Takeo, M. / Higuchi, Y. / Negoro, S.
History
DepositionMay 26, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-aminohexanoate-cyclic-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3552
Polymers52,2631
Non-polymers921
Water8,017445
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 6-aminohexanoate-cyclic-dimer hydrolase
hetero molecules

A: 6-aminohexanoate-cyclic-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7104
Polymers104,5262
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area3860 Å2
ΔGint-12 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.750, 130.750, 58.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein 6-aminohexanoate-cyclic-dimer hydrolase / Nylon oligomers-degrading enzyme EI


Mass: 52262.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: KI72
Description: This bacterium had been called Flavobacterium sp. but reassigned to Arthrobacter strain
Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P13398, 6-aminohexanoate-cyclic-dimer hydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0M sodium citrate, 25% (v/v) glycerol, 0.1M imidazole buffer pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 44300 / Num. obs: 44300 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 69.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 5.1 / Num. unique all: 4021 / % possible all: 90.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→34.49 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2092520.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4446 10.1 %RANDOM
Rwork0.181 ---
obs0.181 44209 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.885 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.85 Å20 Å20 Å2
2---7.85 Å20 Å2
3---15.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 6 445 4052
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.722
X-RAY DIFFRACTIONc_mcangle_it2.383
X-RAY DIFFRACTIONc_scbond_it3.684
X-RAY DIFFRACTIONc_scangle_it4.996
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 413 10.3 %
Rwork0.262 3580 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION4mes.param

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