[English] 日本語
Yorodumi
- PDB-9qyu: Crystal structure of leaf branch compost cutinase quintuple varia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qyu
TitleCrystal structure of leaf branch compost cutinase quintuple variant ICCG L50Y
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / cutinase / PET depolymerase
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Leaf-branch compost cutinase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBischoff, D. / Walla, B. / Dietrich, A.-M. / Janowski, R. / Niessing, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE2715/14-2 Germany
CitationJournal: Bioengineering (Basel) / Year: 2025
Title: Application of a Rational Crystal Contact Engineering Strategy on a Poly(ethylene terephthalate)-Degrading Cutinase.
Authors: Walla, B. / Dietrich, A.M. / Brames, E. / Bischoff, D. / Fritzsche, S. / Castiglione, K. / Janowski, R. / Niessing, D. / Weuster-Botz, D.
History
DepositionApr 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9948
Polymers27,5861
Non-polymers4087
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint3 kcal/mol
Surface area9930 Å2
Unit cell
Length a, b, c (Å)96.65, 96.65, 73.71
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Leaf-branch compost cutinase / LC-cutinase / LCC / PET-digesting enzyme / Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase


Mass: 27585.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 10 mM Tris, 150 mM NaCl, 0.6 M succinic acid, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→48.56 Å / Num. obs: 1098150 / % possible obs: 100 % / Redundancy: 19.88 % / CC1/2: 1 / Net I/σ(I): 25.82
Reflection shellResolution: 1.51→1.6 Å / Num. unique obs: 8798 / CC1/2: 0.678

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
XDSJun 30, 2024data reduction
XDSJun 30, 2024data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→48.325 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.099 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.058 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1836 2763 5.002 %
Rwork0.1494 52479 -
all0.151 --
obs-55242 99.987 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.521 Å2
Baniso -1Baniso -2Baniso -3
1-1.121 Å2-0 Å2-0 Å2
2--1.121 Å2-0 Å2
3----2.243 Å2
Refinement stepCycle: LAST / Resolution: 1.51→48.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 25 205 2173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122045
X-RAY DIFFRACTIONr_angle_refined_deg1.591.7872791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.004517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78710288
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2741086
X-RAY DIFFRACTIONr_chiral_restr0.1050.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021595
X-RAY DIFFRACTIONr_nbd_refined0.2110.2969
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2153
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.212
X-RAY DIFFRACTIONr_mcbond_it6.6253.041042
X-RAY DIFFRACTIONr_mcangle_it8.8095.481306
X-RAY DIFFRACTIONr_scbond_it9.3633.2941003
X-RAY DIFFRACTIONr_scangle_it11.8355.9621485
X-RAY DIFFRACTIONr_lrange_it15.37834.2723192
X-RAY DIFFRACTIONr_rigid_bond_restr5.07832045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.51-1.5490.3412010.30138050.30340080.9410.96399.95010.304
1.549-1.5910.3081960.26737200.26939160.9450.9731000.267
1.591-1.6380.2631910.24636400.24738310.9720.9771000.238
1.638-1.6880.241860.19235380.19437240.9730.9871000.178
1.688-1.7430.2011790.17134010.17235800.9770.9891000.151
1.743-1.8040.1831750.13833140.1434890.9810.9921000.116
1.804-1.8720.1651690.11132130.11433820.9830.9941000.09
1.872-1.9490.1531610.10130610.10432220.9870.9951000.083
1.949-2.0350.161560.1129690.11231250.9850.9941000.096
2.035-2.1340.1661500.12228510.12430020.9850.99399.96670.108
2.134-2.2490.1861430.12927070.13228500.9790.9911000.117
2.249-2.3860.161350.1225650.12227010.9820.99399.9630.111
2.386-2.550.1921270.13324190.13625460.9760.991000.127
2.55-2.7530.1861200.15122690.15323890.9810.9871000.147
2.753-3.0150.1961090.15820750.1621840.9760.9851000.16
3.015-3.370.2081000.16719150.16920150.9760.9841000.178
3.37-3.8880.172900.15717020.15817920.980.9861000.178
3.888-4.7540.13760.11914480.11915240.990.9921000.145
4.754-6.690.218620.16811640.17112260.9790.9871000.206
6.69-48.3250.184370.1837030.1837400.9890.9861000.243

+
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