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- PDB-1wyb: Structure of 6-aminohexanoate-dimer hydrolase -

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Basic information

Entry
Database: PDB / ID: 1wyb
TitleStructure of 6-aminohexanoate-dimer hydrolase
Components6-aminohexanoate-dimer hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


6-aminohexanoate-oligomer exohydrolase / 6-aminohexanoate-dimer hydrolase activity / nylon catabolic process
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #420 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #710 / : / Beta-lactamase-related / Beta-lactamase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #420 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #710 / : / Beta-lactamase-related / Beta-lactamase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Beta-lactamase/transpeptidase-like / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 6-aminohexanoate-dimer hydrolase
Similarity search - Component
Biological speciesFlavobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsNegoro, S. / Ohki, T. / Shibata, N. / Mizuno, N. / Wakitani, Y. / Tsurukame, J. / Matsumoto, K. / Kawamoto, I. / Takeo, M. / Higuchi, Y.
CitationJournal: To be Published
Title: Structure of 6-aminohexanoate-dimer hydrolase
Authors: Negoro, S. / Ohki, T. / Shibata, N. / Mizuno, N. / Wakitani, Y. / Tsurukame, J. / Matsumoto, K. / Kawamoto, I. / Takeo, M. / Higuchi, Y.
History
DepositionFeb 9, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 6-aminohexanoate-dimer hydrolase


Theoretical massNumber of molelcules
Total (without water)42,8391
Polymers42,8391
Non-polymers00
Water7,476415
1


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

A: 6-aminohexanoate-dimer hydrolase


Theoretical massNumber of molelcules
Total (without water)85,6792
Polymers85,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5140 Å2
ΔGint-25 kcal/mol
Surface area28000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.370, 96.370, 113.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 6-aminohexanoate-dimer hydrolase


Mass: 42839.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. (bacteria) / Strain: KI72 / Plasmid: pKP1500 / Production host: Escherichia coli (E. coli)
References: UniProt: P07062, GenBank: 488342, 6-aminohexanoate-oligomer exohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.11 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, lithium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→27.97 Å / Num. all: 57052 / Num. obs: 57052 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.082 / Net I/σ(I): 7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 1.7 / Num. unique all: 8227 / Rsym value: 0.439 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2359099.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5760 10.2 %RANDOM
Rwork0.185 ---
obs0.185 56644 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.849 Å2 / ksol: 0.390834 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.37 Å20 Å2
2---0.59 Å20 Å2
3---1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 0 415 3327
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 561 10.1 %
Rwork0.251 4987 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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