[English] 日本語
Yorodumi
- PDB-2zma: Crystal Structure of 6-Aminohexanoate-dimer Hydrolase S112A/G181D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zma
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
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 / Beta-lactamase/transpeptidase-like ...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 / Beta-lactamase/transpeptidase-like / Special / 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 sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.51 Å
AuthorsOhki, T. / Shibata, N. / Higuchi, Y. / Takeo, M. / Negoro, S.
CitationJournal: Febs J. / Year: 2009
Title: Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold
Authors: Kawashima, Y. / Ohki, T. / Shibata, N. / Higuchi, Y. / Wakitani, Y. / Matsuura, Y. / Nakata, Y. / Takeo, M. / Kato, D. / Negoro, S.
History
DepositionApr 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / 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 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,30414
Polymers42,9061
Non-polymers1,39813
Water7,746430
1
A: 6-aminohexanoate-dimer hydrolase
hetero molecules

A: 6-aminohexanoate-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,60828
Polymers85,8112
Non-polymers2,79726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area11920 Å2
ΔGint-107.5 kcal/mol
Surface area27130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.687, 96.687, 112.911
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-860-

HOH

-
Components

-
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 sp. (bacteria) / Gene: nylB, nylB' / Plasmid: PKP1500 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KP3998
References: UniProt: P07061, UniProt: P07062, 6-aminohexanoate-oligomer exohydrolase

-
Non-polymers , 5 types, 443 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.36 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. all: 96045 / Num. obs: 96045 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 31.7
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.2 / Num. unique all: 9326 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DCF

2dcf


Resolution: 1.51→33.63 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 157420.7 / 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
Rfree0.19 9186 10 %RANDOM
Rwork0.175 ---
obs0.175 92254 96.2 %-
all-92254 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.1612 Å2 / ksol: 0.392279 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.28 Å20 Å2
2--0.33 Å20 Å2
3----0.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.51→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 84 430 3478
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
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_it1.632
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.51→1.56 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.254 798 9.4 %
Rwork0.248 7652 -
obs--89 %
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more