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- PDB-2dcf: Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D... -

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Basic information

Entry
Database: PDB / ID: 2dcf
TitleCrystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N mutant with substrate
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-AMINOHEXANOIC ACID / 6-aminohexanoate-dimer hydrolase / 6-aminohexanoate-dimer hydrolase / 6-aminohexanoate-dimer hydrolase
Similarity search - Component
Biological speciesFlavobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsOhki, T. / Shibata, N. / Higuchi, Y. / Takeo, M. / Negoro, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase
Authors: Negoro, S. / Ohki, T. / Shibata, N. / Sasa, K. / Hayashi, H. / Nakano, H. / Yasuhira, K. / Kato, D. / Takeo, M. / Higuchi, Y.
History
DepositionJan 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,87610
Polymers42,8571
Non-polymers1,0189
Water8,629479
1


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

A: 6-aminohexanoate-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,75120
Polymers85,7152
Non-polymers2,03618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area10180 Å2
ΔGint-61 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.620, 96.620, 112.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 6-aminohexanoate-dimer hydrolase


Mass: 42857.488 Da / Num. of mol.: 1 / Mutation: S112A/G181D/H266N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. (bacteria) / Plasmid: pKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): KP3998
References: UniProt: P07061, UniProt: Q59710, UniProt: P07062*PLUS, 6-aminohexanoate-oligomer exohydrolase

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Non-polymers , 5 types, 488 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Comment: inhibitor*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 479 / 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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.2M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, 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: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 119444 / Num. obs: 119444 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.1 Å2
Reflection shellResolution: 1.4→1.45 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1WYB

1wyb


Resolution: 1.4→39.22 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 95436.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.195 11680 10 %RANDOM
Rwork0.183 ---
obs0.183 116862 97.6 %-
all-119444 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.8144 Å2 / ksol: 0.393825 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.4→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 58 479 3497
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_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.32.5
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.246 1080 9.7 %
Rwork0.232 10024 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4mes.paramsub.top

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