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- PDB-3vwl: Crystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187S... -

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Basic information

Entry
Database: PDB / ID: 3vwl
TitleCrystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187S/H266N/D370Y mutant
Components6-aminohexanoate-dimer hydrolase
KeywordsHYDROLASE / NYLON DEGRADATION
Function / homology
Function and homology information


6-aminohexanoate-oligomer exohydrolase / 6-aminohexanoate-dimer hydrolase activity / nylon catabolic process
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #710 / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Beta-lactamase/transpeptidase-like / Up-down Bundle / 3-Layer(aba) Sandwich ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #710 / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Beta-lactamase/transpeptidase-like / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-aminohexanoate-dimer hydrolase / 6-aminohexanoate-dimer hydrolase / 6-aminohexanoate-dimer hydrolase
Similarity search - Component
Biological speciesFlavobacterium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsKawashima, Y. / Shibata, N. / Negoro, S. / Higuchi, Y.
CitationJournal: To be Published
Title: Structural, kinetic and theoretical analyses of hydrolase mutants altering in the directionality and equilibrium point of reversible amide-synthetic/hydrolytic reaction
Authors: Negoro, S. / Kawashima, Y. / Shibata, N. / Shigeta, Y. / Kobayashi, T. / Nishiguchi, H. / Matsui, T. / Baba, T. / Lee, Y. / Kamiya, K. / Kato, D. / Takeo, M. / Higuchi, Y.
History
DepositionAug 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,18612
Polymers42,8511
Non-polymers1,33411
Water7,656425
1
A: 6-aminohexanoate-dimer hydrolase
hetero molecules

A: 6-aminohexanoate-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,37224
Polymers85,7032
Non-polymers2,66922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area11480 Å2
ΔGint-83 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.430, 96.430, 113.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-729-

HOH

21A-924-

HOH

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Components

#1: Protein 6-aminohexanoate-dimer hydrolase / Nylon oligomers-degrading enzyme EII / Nylon oligomers-degrading enzyme EII'


Mass: 42851.457 Da / Num. of mol.: 1 / Mutation: G181D, R187S, H266N, D370Y
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF RESIDUES 1-21 FROM NYLON OLIGOMERS-DEGRADING ENZYME EII (UNP P07061) AND RESIDUES 22-392 FROM NYLON OLIGOMERS-DEGRADING ENZYME EII' (UNP Q59710)
Source: (gene. exp.) Flavobacterium (bacteria) / Strain: K172, KI723T1 / Gene: nylB, nylB' / Plasmid: PKP1500 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KP3998
References: UniProt: P07061, UniProt: Q59710, UniProt: P07062*PLUS, 6-aminohexanoate-oligomer exohydrolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 65.27 % / Mosaicity: 0.3 °
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 26, 2009
RadiationMonochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→24.39 Å / Num. obs: 80217 / % possible obs: 99.7 % / Redundancy: 2.96 % / Rmerge(I) obs: 0.041 / Χ2: 0.6 / Net I/σ(I): 11.5 / Scaling rejects: 1792
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.6-1.662.530.3532.21985677660.7820597.5
1.66-1.722.880.28332329379910.75285100
1.72-1.82.930.2033.92341279510.65112100
1.8-1.92.950.1425.52365879550.6418299.9
1.9-2.022.990.17.32408380190.6125100
2.02-2.173.010.079.92417879760.5615999.9
2.17-2.393.040.054122460880320.5316199.9
2.39-2.733.080.04215.22491880680.5198100
2.73-3.443.080.03212524681260.518299.9
3.44-24.393.040.02330.72562983330.5428399.7

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata reduction
CNS1.2refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→24.39 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 444577 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.209 7892 10 %RANDOM
Rwork0.19 ---
obs-78844 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.5122 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 83.29 Å2 / Biso mean: 22.1303 Å2 / Biso min: 8.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.6→24.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 81 425 3466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it4.42
X-RAY DIFFRACTIONc_scangle_it5.962.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.411 671 9.1 %
Rwork0.423 6721 -
all-7392 -
obs--92.8 %
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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