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- PDB-3a66: Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D... -

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Basic information

Entry
Database: PDB / ID: 3a66
TitleCrystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N/D370Y mutant with substrate
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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-AMINOHEXANOIC ACID / 6-aminohexanoate-dimer hydrolase / 6-aminohexanoate-dimer hydrolase
Similarity search - Component
Biological speciesFlavobacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKawashima, Y. / Shibata, N. / Higuchi, Y. / Takeo, M. / Negoro, S.
CitationJournal: To be Published
Title: Enzymatic Synthesis of Nylon-6 Units in Organic Sol Contained Low-Water: Structural Requirement of 6-Aminohexanoate-Dimer Hydrolase for Efficient Amid Synthesis
Authors: Kawashima, Y. / Yasuhira, K. / Shibata, N. / Matsuura, Y. / Tanaka, Y. / Taniguchi, M. / Miyoshi, Y. / Takeo, M. / Kato, D. / Higuchi, Y. / Negoro, S.
History
DepositionAug 21, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
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

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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)44,11813
Polymers42,9061
Non-polymers1,21212
Water7,206400
1
A: 6-AMINOHEXANOATE-DIMER HYDROLASE
hetero molecules

A: 6-AMINOHEXANOATE-DIMER HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,23626
Polymers85,8112
Non-polymers2,42524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area11340 Å2
ΔGint-47 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.524, 96.524, 113.089
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-393-

HOH

21A-395-

HOH

31A-804-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 6-AMINOHEXANOATE-DIMER HYDROLASE / NYLON OLIGOMERS-DEGRADING ENZYME EII / NYLON OLIGOMERS-DEGRADING ENZYME EII'


Mass: 42905.574 Da / Num. of mol.: 1 / Mutation: S112A, G181D, H266N, D370Y
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF NYLON OLIGOMERS-DEGRADING ENZYME EII (RESIDUES 1-21) AND NYLON OLIGOMERS-DEGRADING ENZYME EII' (RESIDUES 22-392)
Source: (gene. exp.) Flavobacterium (bacteria) / Strain: K172
Description: Strain of the source organism is described KI72 in the first reference of the d atabase UniProtKB/Swiss-Prot P07061 (NYLB_FLASK) and P07062 (NYLC_FLASK).
Gene: nylB, NYLB' / Plasmid: PKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): KP3998
References: UniProt: P07061, UniProt: P07062, 6-aminohexanoate-oligomer exohydrolase

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Non-polymers , 5 types, 412 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsACCORDING TO DEPOSITORS, ARG190 AND HIS191 ARE CORRECT AND SWISSPROT IS INCORRECT AT THESE POSITIONS.

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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: 65.3 %
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 6.50, 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
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 28, 2008
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→27.99 Å / Num. obs: 79800 / % possible obs: 98.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 10 / Redundancy: 3.23 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.6 / % possible all: 92.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNS1.2refinement
d*TREKdata reduction
d*TREKdata scaling
CNS1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZM0

2zm0


Resolution: 1.6→27.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 614650.02 / 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
Rfree0.225 7870 10 %RANDOM
Rwork0.21 ---
obs0.21 78616 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.3169 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 77 400 3394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.429 668 9.4 %
Rwork0.433 6422 -
obs--88.8 %
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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