[English] 日本語
Yorodumi
- PDB-6ilx: Crystal structure of PETase W159F mutant from Ideonella sakaiensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ilx
TitleCrystal structure of PETase W159F mutant from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / Mutation
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsLiu, C.C. / Shi, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570732 China
National Natural Science Foundation of China31770785 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural and functional characterization of polyethylene terephthalate hydrolase from Ideonella sakaiensis.
Authors: Liu, C. / Shi, C. / Zhu, S. / Wei, R. / Yin, C.C.
History
DepositionOct 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title

-
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)28,5603
Polymers28,5021
Non-polymers582
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area10360 Å2
Unit cell
Length a, b, c (Å)51.087, 51.077, 85.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 28501.611 Da / Num. of mol.: 1 / Mutation: W159F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria)
Strain: 201-F6 / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris, pH 5.5, 3M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 37628 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.485 / Rpim(I) all: 0.202 / Rrim(I) all: 0.526 / Rsym value: 1.114 / Net I/σ(I): 3.53
Reflection shellResolution: 2.2→2.24 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.45→43.838 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.18
RfactorNum. reflection% reflection
Rfree0.1951 1900 5.05 %
Rwork0.169 --
obs0.1703 37628 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→43.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 2 139 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082001
X-RAY DIFFRACTIONf_angle_d1.0322726
X-RAY DIFFRACTIONf_dihedral_angle_d11.878712
X-RAY DIFFRACTIONf_chiral_restr0.091299
X-RAY DIFFRACTIONf_plane_restr0.008361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.217810.14851739X-RAY DIFFRACTION64
1.4863-1.52650.21461100.15371974X-RAY DIFFRACTION74
1.5265-1.57140.20761060.14772227X-RAY DIFFRACTION83
1.5714-1.62210.19251390.15562514X-RAY DIFFRACTION93
1.6221-1.68010.20971470.15782663X-RAY DIFFRACTION98
1.6801-1.74730.20691390.1482664X-RAY DIFFRACTION99
1.7473-1.82690.18961460.14772677X-RAY DIFFRACTION98
1.8269-1.92320.18881690.15142641X-RAY DIFFRACTION99
1.9232-2.04370.18931180.16172730X-RAY DIFFRACTION98
2.0437-2.20150.20371390.16592709X-RAY DIFFRACTION100
2.2015-2.4230.18751410.18252754X-RAY DIFFRACTION100
2.423-2.77360.21061420.19362743X-RAY DIFFRACTION100
2.7736-3.49420.21971670.19232772X-RAY DIFFRACTION100
3.4942-43.85840.16421560.1582921X-RAY DIFFRACTION100

+
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