[English] 日本語
Yorodumi
- PDB-7cts: Open form of PET-degrading cutinase Cut190 with thermostability-i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cts
TitleOpen form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation
ComponentsAlpha/beta hydrolase family protein
KeywordsHYDROLASE / PROTEIN ENGINEERING / POLYESTERASE / disulfide bond / metal binding
Function / homologyPlatelet-activating factor acetylhydrolase, isoform II / Cutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / 1,4-DIETHYLENE DIOXIDE / Cutinase
Function and homology information
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsEmori, M. / Numoto, N. / Senga, A. / Bekker, G.J. / Kamiya, N. / Ito, N. / Kawai, F. / Oda, M.
CitationJournal: Proteins / Year: 2021
Title: Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability.
Authors: Emori, M. / Numoto, N. / Senga, A. / Bekker, G.J. / Kamiya, N. / Kobayashi, Y. / Ito, N. / Kawai, F. / Oda, M.
History
DepositionAug 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: 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 6, 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: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1814
Polymers28,8901
Non-polymers2913
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-12 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.623, 64.984, 78.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 Alpha/beta hydrolase family protein / Cutinase


Mass: 28889.537 Da / Num. of mol.: 1
Mutation: S226P, R228S, Q138A, D250C, E296C, Q123H, N202H, S176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Gene: Cut190, SAMN02982918_2340 / Plasmid: PQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA-GAMI B (DE3) / References: UniProt: W0TJ64, cutinase
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bicine, 2% (v/v) 1,4-dioxane, 10% (w/v) PEG 20000

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→31 Å / Num. obs: 125717 / % possible obs: 96 % / Redundancy: 5.8 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 0.999 / Rsym value: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 1.1→1.16 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 19227 / CC1/2: 0.599 / Rsym value: 1.06

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFJ

4wfj


Resolution: 1.1→30.02 Å / SU ML: 0.1294 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7348 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1624 6281 5 %
Rwork0.142 119414 -
obs0.143 125695 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.92 Å2
Refinement stepCycle: LAST / Resolution: 1.1→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 18 445 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912117
X-RAY DIFFRACTIONf_angle_d1.16442885
X-RAY DIFFRACTIONf_chiral_restr0.0953310
X-RAY DIFFRACTIONf_plane_restr0.0098378
X-RAY DIFFRACTIONf_dihedral_angle_d13.1946788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.34452130.3143554X-RAY DIFFRACTION87.77
1.11-1.120.31711680.30263837X-RAY DIFFRACTION92.67
1.12-1.140.32762060.28993836X-RAY DIFFRACTION92.9
1.14-1.150.25732000.2653806X-RAY DIFFRACTION93.4
1.15-1.170.28061840.25983787X-RAY DIFFRACTION91.77
1.17-1.180.2751980.25523849X-RAY DIFFRACTION93.08
1.18-1.20.2452140.22443823X-RAY DIFFRACTION93.71
1.2-1.220.23471910.20733848X-RAY DIFFRACTION93.93
1.22-1.240.22542130.19563890X-RAY DIFFRACTION94.39
1.24-1.260.22661970.18123954X-RAY DIFFRACTION95.29
1.26-1.280.18682100.17653901X-RAY DIFFRACTION95.4
1.28-1.30.20952150.16553936X-RAY DIFFRACTION95.6
1.3-1.330.16682050.15753950X-RAY DIFFRACTION95.8
1.33-1.350.19372130.1523949X-RAY DIFFRACTION96.21
1.35-1.380.16071980.14763978X-RAY DIFFRACTION96.33
1.38-1.420.17172220.13754005X-RAY DIFFRACTION96.55
1.42-1.450.14092080.12573971X-RAY DIFFRACTION96.76
1.45-1.490.15292180.11754001X-RAY DIFFRACTION97.08
1.49-1.530.14761990.1084049X-RAY DIFFRACTION97.14
1.53-1.580.13422220.1034020X-RAY DIFFRACTION97.36
1.58-1.640.12512140.1044061X-RAY DIFFRACTION97.85
1.64-1.710.14272060.10774047X-RAY DIFFRACTION97.55
1.71-1.780.15012200.11684079X-RAY DIFFRACTION98.35
1.78-1.880.16582170.12374070X-RAY DIFFRACTION97.97
1.88-1.990.15642140.11434095X-RAY DIFFRACTION98.2
1.99-2.150.14782130.1194139X-RAY DIFFRACTION98.62
2.15-2.360.13612200.12314142X-RAY DIFFRACTION98.91
2.36-2.710.13712220.13164206X-RAY DIFFRACTION99.3
2.71-3.410.13492270.14134234X-RAY DIFFRACTION99.46
3.41-30.020.16522340.14394397X-RAY DIFFRACTION99.16

+
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