[English] 日本語
Yorodumi
- PDB-8etz: Ancestral PETase 35_442 Mutant E13D -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8etz
TitleAncestral PETase 35_442 Mutant E13D
ComponentsPolyethylene terephthalate hydrolase
KeywordsHYDROLASE / PET / PETase / Plastic degradation / Ancestral Sequence Reconstruction
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSaunders, J.W. / Frkic, R.L. / Jackson, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Ancestral PETase 35_442 Mutant E13D
Authors: Saunders, J. / Frkic, R.L. / Jackson, C.J.
History
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyethylene terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,15213
Polymers30,1081
Non-polymers1,04412
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.533, 149.488, 55.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-304-

EDO

21A-536-

HOH

31A-612-

HOH

41A-620-

HOH

51A-648-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Polyethylene terephthalate hydrolase


Mass: 30108.232 Da / Num. of mol.: 1 / Mutation: E13D
Source method: isolated from a genetically manipulated source
Details: Ancestral PETase 35_442 Mutant E13D / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 6 types, 270 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.68→41.71 Å / Num. obs: 33515 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 22.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.052 / Rrim(I) all: 0.186 / Net I/σ(I): 11.2 / Num. measured all: 433610 / Scaling rejects: 1236
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.7112.74.6122161116960.4711.3394.8051100
9.05-41.71110.06228082550.9980.0190.06537.299.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QGC

6qgc


Resolution: 1.68→41.71 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1738 1659 4.96 %
Rwork0.1547 31806 -
obs0.1556 33465 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.98 Å2 / Biso mean: 28.3937 Å2 / Biso min: 13.61 Å2
Refinement stepCycle: final / Resolution: 1.68→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 164 258 2390
Biso mean--53.75 36.69 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.68-1.730.30991340.30225912725
1.73-1.790.29121450.26826052750
1.79-1.850.2921420.236426102752
1.85-1.920.22511420.194626162758
1.92-2.010.21761450.168425892734
2.01-2.120.15751260.154426772803
2.12-2.250.17671480.140825942742
2.25-2.420.17231230.137226772800
2.42-2.670.16811410.140126542795
2.67-3.050.18441190.142326872806
3.05-3.840.14141250.134227072832
3.85-41.710.14661690.147727992968
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)
14.67940.5558-2.21421.934-1.76754.8225-0.02720.1516-0.1542-0.1955-0.07780.0386-0.0130.08670.11370.1910.0106-0.03920.1786-0.03940.135816.8039-0.51027.0563
20.96070.35440.00653.12640.8972.0067-0.06620.0830.1979-0.1343-0.00560.2521-0.1018-0.10570.07890.20160.0088-0.04390.22230.03230.24738.867317.92129.9216
33.84741.89431.62845.24991.77621.7399-0.0884-0.10880.3294-0.0487-0.07070.5825-0.1452-0.11010.1830.16330.00480.00230.19580.02660.23423.27614.572616.9758
41.61780.21360.15322.2906-0.34541.215-0.0161-0.07640.19920.1186-0.0541-0.0322-0.16670.06960.06760.1732-0.0063-0.01650.17420.00130.164422.348816.384721.3317
53.3429-0.550.98250.1413-0.17710.2932-0.01080.1102-0.1407-0.00960.0310.0282-0.04050.0553-0.03590.2081-0.00890.00370.2575-0.01450.191730.5126-4.730917.0454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 96 )A26 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 125 )A97 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 232 )A126 - 232
5X-RAY DIFFRACTION5chain 'A' and (resid 233 through 261 )A233 - 261

+
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