[English] 日本語
Yorodumi
- PDB-3vwm: Crystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vwm
TitleCrystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187A/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

-
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)44,07411
Polymers42,8351
Non-polymers1,23810
Water7,656425
1
A: 6-aminohexanoate-dimer hydrolase
hetero molecules

A: 6-aminohexanoate-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,14822
Polymers85,6712
Non-polymers2,47720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area11030 Å2
ΔGint-46 kcal/mol
Surface area27340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.220, 96.220, 113.150
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-533-

HOH

21A-887-

HOH

31A-923-

HOH

-
Components

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


Mass: 42835.461 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.: 2 / 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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.15 % / 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

-
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 27, 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→27.96 Å / Num. obs: 79765 / % possible obs: 99.5 % / Redundancy: 4.49 % / Rmerge(I) obs: 0.038 / Χ2: 0.7 / Net I/σ(I): 16 / Scaling rejects: 2707
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.6-1.663.730.3513.1292067744129897.8
1.66-1.724.260.2664.13407178710.9156999.2
1.72-1.84.310.1685.93425379020.723099.6
1.8-1.94.380.1247.53495579280.6827099.7
1.9-2.024.460.0910.13572779400.6731499.7
2.02-2.174.560.06613.13644979450.6524299.7
2.17-2.394.670.05216.43753679980.6220799.9
2.39-2.744.810.04120.83884580280.6120999.9
2.74-3.454.860.02830.13964681210.6117699.9
3.45-27.964.820.02240.14012982880.6419299.5

-
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→27.96 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 630547 / 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
Rfree0.218 7947 10 %RANDOM
Rwork0.193 ---
obs-79315 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0647 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 86.45 Å2 / Biso mean: 22.309 Å2 / Biso min: 8.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--1.07 Å20 Å2
3----2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 76 425 3460
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it4.442
X-RAY DIFFRACTIONc_scangle_it5.892.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.445 740 9.7 %
Rwork0.441 6873 -
all-7613 -
obs--96.1 %
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

+
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://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