[English] 日本語
Yorodumi
- PDB-7ym9: Crystal structure of a PET hydrolase from Cryptosporangium aurantiacum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ym9
TitleCrystal structure of a PET hydrolase from Cryptosporangium aurantiacum
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / Poly(Ethylene terephthalate) hydrolase / esterase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / MALONATE ION / PET hydrolase/cutinase-like domain-containing protein
Function and homology information
Biological speciesCryptosporangium aurantiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsHong, H. / Ki, D. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Discovery and rational engineering of PET hydrolase with both mesophilic and thermophilic PET hydrolase properties.
Authors: Hong, H. / Ki, D. / Seo, H. / Park, J. / Jang, J. / Kim, K.J.
History
DepositionJul 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
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: Poly(ethylene terephthalate) hydrolase
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1334
Polymers57,9292
Non-polymers2042
Water8,467470
1
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0662
Polymers28,9641
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0662
Polymers28,9641
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.309, 82.449, 87.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Poly(ethylene terephthalate) hydrolase


Mass: 28964.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporangium aurantiacum (bacteria)
Gene: SAMN05443668_101498 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M7II12
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% (w/v) PEG3350, 0.1 M Sodium malonate pH4.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 133383 / % possible obs: 99.9 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Χ2: 2.308 / Net I/σ(I): 10 / Num. measured all: 1647419
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.34-1.3610.40.51266050.9480.1640.5381.446100
1.36-1.3912.30.49366010.9660.1460.5151.499100
1.39-1.4112.40.43566120.9710.1280.4541.588100
1.41-1.4412.50.38666010.9740.1130.4021.651100
1.44-1.4712.50.33566230.980.0980.3491.745100
1.47-1.5112.60.29566100.9840.0860.3071.855100
1.51-1.5512.60.25665990.9870.0750.2671.989100
1.55-1.5912.60.22966230.9880.0670.2392.1100
1.59-1.6412.60.20666190.9890.060.2142.171100
1.64-1.6912.70.18366460.9920.0530.1912.269100
1.69-1.7512.70.16166460.9930.0470.1682.388100
1.75-1.8212.60.14166560.9950.0410.1472.542100
1.82-1.912.60.12366270.9950.0360.1282.729100
1.9-212.60.10866980.9960.0320.1132.828100
2-2.1312.60.09566430.9960.0280.0992.924100
2.13-2.2912.60.08667210.9970.0250.092.95100
2.29-2.5212.60.07767090.9970.0220.082.874100
2.52-2.8912.50.06767370.9980.020.072.759100
2.89-3.6412.20.05768510.9980.0170.062.775100
3.64-5010.80.05369560.9970.0170.0562.88998.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LUL

5lul


Resolution: 1.34→26.23 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.661 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1827 6373 4.8 %RANDOM
Rwork0.1721 ---
obs0.1726 126891 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.57 Å2 / Biso mean: 13.757 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0 Å2
2---0.8 Å20 Å2
3---0.28 Å2
Refinement stepCycle: final / Resolution: 1.34→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 14 470 4386
Biso mean--24.69 23.87 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134097
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143720
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.6475625
X-RAY DIFFRACTIONr_angle_other_deg1.5811.5728555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39220.99202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74415563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1531530
X-RAY DIFFRACTIONr_chiral_restr0.1150.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021017
LS refinement shellResolution: 1.34→1.375 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 505 -
Rwork0.214 9152 -
all-9657 -
obs--98.55 %

+
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