[English] 日本語
Yorodumi
- PDB-6qgc: PETase from Ideonella sakaiensis without ligand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qgc
TitlePETase from Ideonella sakaiensis without ligand
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET degradation
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPalm, G.J. / Reisky, L. / Boettcher, D. / Mueller, H. / Michels, E.A.P. / Walczak, C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate.
Authors: Palm, G.J. / Reisky, L. / Bottcher, D. / Muller, H. / Michels, E.A.P. / Walczak, M.C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,51311
Polymers121,0834
Non-polymers4307
Water8,179454
1
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4023
Polymers30,2711
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3062
Polymers30,2711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4984
Polymers30,2711
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3062
Polymers30,2711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.121, 78.769, 140.121
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 30270.783 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1 ul protein (10 mg/ml, 20 mM TRIS pH 7.5, 150 mM NaCl) + 1 ul reservoir (0.1 M sodium citrate or sodium acetate pH 5.0, 15% (v/v) PEG8000, 0.5 M lithium sulfate)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9799 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 73090 / % possible obs: 97.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.1 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.151 / Rsym value: 0.131 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11574 / CC1/2: 0.62 / Rrim(I) all: 0.838 / Rsym value: 0.719 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSJun 1, 2017data reduction
XDSJun 1, 2017data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CG1

4cg1


Resolution: 2→48.73 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.568 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26091 3607 4.9 %RANDOM
Rwork0.21347 ---
obs0.21578 69684 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.386 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å2-0 Å20.33 Å2
2---2.11 Å20 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 2→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7689 0 19 454 8162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0147902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176728
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.65610780
X-RAY DIFFRACTIONr_angle_other_deg1.0521.63415832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40651048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80221.556360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.874151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4021552
X-RAY DIFFRACTIONr_chiral_restr0.0860.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021473
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3850.814186
X-RAY DIFFRACTIONr_mcbond_other0.3850.814185
X-RAY DIFFRACTIONr_mcangle_it0.6581.2135227
X-RAY DIFFRACTIONr_mcangle_other0.6581.2135228
X-RAY DIFFRACTIONr_scbond_it0.5870.8843716
X-RAY DIFFRACTIONr_scbond_other0.5170.8723703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8261.2875532
X-RAY DIFFRACTIONr_long_range_B_refined4.46710.3118831
X-RAY DIFFRACTIONr_long_range_B_other4.40110.0618766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 262 -
Rwork0.303 4823 -
obs--91.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0663-0.2222-0.14870.6538-0.07750.4528-0.00190.0574-0.0479-0.02910.00730.0502-0.00030.0275-0.00540.0067-0.0057-0.03730.2332-0.00710.251810.355-14.618194.083
20.6480.18-0.21040.6553-0.21320.52540.0227-0.0691-0.02590.073-0.00540.0264-0.02870.0303-0.01730.0129-0.004-0.03150.2326-0.00560.261835.697-12.424222.624
31.0816-0.3261-0.06780.80370.0640.48280.03430.06020.0458-0.0509-0.0059-0.0301-0.0398-0.0364-0.02840.01270.0054-0.0370.2203-0.0010.257418.883-29.573264.311
40.6043-0.09730.20660.5982-0.13740.48210.01110.0584-0.0148-0.0695-0.01630.02120.02590.03310.00520.01640.004-0.04730.2291-0.00190.254632.5647.468267.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 290
2X-RAY DIFFRACTION2B29 - 289
3X-RAY DIFFRACTION3C28 - 289
4X-RAY DIFFRACTION4D29 - 289

+
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