[English] 日本語
Yorodumi
- PDB-8vem: IsPETase - ACCE mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vem
TitleIsPETase - ACCE mutant
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / protein engineering
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesPiscinibacter sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.711 Å
AuthorsJoho, Y. / Royan, S. / Newton, S. / Caputo, A.T. / Ardevol Grau, A. / Jackson, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: Chembiochem / Year: 2024
Title: Enhancing PET Degrading Enzymes: A Combinatory Approach.
Authors: Joho, Y. / Royan, S. / Caputo, A.T. / Newton, S. / Peat, T.S. / Newman, J. / Jackson, C. / Ardevol, A.
History
DepositionDec 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7132
Polymers28,6171
Non-polymers961
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.778, 59.085, 78.602
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 28616.830 Da / Num. of mol.: 1 / Mutation: S136E, D186A, N233C, S282C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piscinibacter sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.138 M ammonium sulfate, 30 w/v polyethylene glycol 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.711→47.229 Å / Num. obs: 16551 / % possible obs: 93 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.047 / Rrim(I) all: 0.173 / Net I/σ(I): 11.6
Reflection shellResolution: 1.711→1.858 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.916 / Num. unique obs: 829 / CC1/2: 0.53 / Rpim(I) all: 0.574 / Rrim(I) all: 2.003 / % possible all: 54.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.711→47.23 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 1.712 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 785 -RANDOM
Rwork0.2119 ---
obs0.2136 16551 63.2 %-
Displacement parametersBiso mean: 31.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.7545 Å20 Å20 Å2
2--5.4342 Å20 Å2
3----2.6797 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.711→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 5 181 2108
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083984HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.027183HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1215SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes668HARMONIC5
X-RAY DIFFRACTIONt_it2047HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion285SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3773SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.47
X-RAY DIFFRACTIONt_other_torsion14.22
LS refinement shellResolution: 1.711→1.82 Å
RfactorNum. reflection% reflection
Rfree0.2362 20 -
Rwork0.3059 --
obs--9.54 %
Refinement TLS params.Origin x: -6.7743 Å / Origin y: 1.8124 Å / Origin z: -5.7475 Å
111213212223313233
T-0.1012 Å20.0287 Å20.0243 Å2-0.0823 Å20.0219 Å2---0.1353 Å2
L1.7658 °20.3547 °21.1744 °2-0.9955 °20.2386 °2--3.96 °2
S-0.0049 Å °-0.0771 Å °0.4333 Å °-0.0771 Å °0.0554 Å °0.5148 Å °0.4333 Å °0.5148 Å °-0.0505 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 290
2X-RAY DIFFRACTION1{ A|* }A301

+
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