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- PDB-2zm2: Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F... -

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Basic information

Entry
Database: PDB / ID: 2zm2
TitleStructure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94)
Components6-aminohexanoate-dimer hydrolase
KeywordsHYDROLASE / ALPHA-BETA
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 / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...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 / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / 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
Similarity search - Component
Biological speciesFLAVOBACTERIUM SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOhki, T. / Shibata, N. / Higuchi, Y. / Kawashima, Y. / Takeo, M. / Kato, D. / Nego, S.
CitationJournal: Protein Sci. / Year: 2009
Title: Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.
Authors: Ohki, T. / Shibata, N. / Higuchi, Y. / Kawashima, Y. / Takeo, M. / Kato, D. / Negoro, S.
History
DepositionApr 10, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)44,57314
Polymers42,9441
Non-polymers1,63013
Water8,917495
1
A: 6-aminohexanoate-dimer hydrolase
hetero molecules

A: 6-aminohexanoate-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,14728
Polymers85,8872
Non-polymers3,25926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area12550 Å2
ΔGint-96 kcal/mol
Surface area27650 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.442, 96.442, 113.496
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-910-

HOH

21A-911-

HOH

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Components

#1: Protein 6-aminohexanoate-dimer hydrolase


Mass: 42943.711 Da / Num. of mol.: 1 / Mutation: A61V, A124V, R187S, F264C, G291R, G338A, 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 SP. (bacteria) / Strain: K172 / Gene: NYLB, NYLB' / Plasmid: PKP1500 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P07061, UniProt: P07062, 6-aminohexanoate-oligomer exohydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O
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: 3.55 Å3/Da / Density % sol: 65.33 %
Crystal growTemperature: 283 K / pH: 6.5
Details: 2.2M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, pH 6.50, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 96878 / Num. obs: 96878 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 44.91
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.26 / Num. unique all: 8782 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WYB

1wyb


Resolution: 1.55→33.64 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1845983.03 / 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
Rfree0.192 8876 10 %RANDOM
Rwork0.179 ---
obs0.179 88723 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.0769 Å2 / ksol: 0.387215 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.28 Å20 Å2
2--1 Å20 Å2
3----2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.55→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 97 495 3557
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_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shellResolution: 1.55→1.61 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.234 895 10.2 %
Rwork0.231 7851 -
obs--99.4 %

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