[English] 日本語
Yorodumi
- PDB-7eoa: HR-PETase from Bacterium HR29 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eoa
TitleHR-PETase from Bacterium HR29
ComponentsPoly(Ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / hydrolase activity
Similarity search - Function
Alpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / Poly(Ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesbacterium HR29 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsWang, J. / Wang, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725022 China
CitationJournal: To Be Published
Title: Crystal structure of Bomgl, a monoacylglycerol lipase from marine Bacillus
Authors: Wang, Y.H. / Wang, J. / Lan, D.M.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0363
Polymers27,9441
Non-polymers922
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area10090 Å2
Unit cell
Length a, b, c (Å)52.490, 52.490, 197.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Poly(Ethylene terephthalate) hydrolase


Mass: 27944.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) bacterium HR29 (bacteria) / Gene: HRbin29_00073 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2H5Z9R5, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl pH 8.4, ethanol 19.5% (v/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.24→27.84 Å / Num. obs: 78799 / % possible obs: 99.29 % / Redundancy: 19.3 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.01 / Rrim(I) all: 0.048 / Net I/σ(I): 30.8
Reflection shellResolution: 1.24→1.27 Å / Rmerge(I) obs: 0.428 / Num. unique obs: 5427 / CC1/2: 0.908 / Rpim(I) all: 0.223 / Rrim(I) all: 0.428

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EB0

4eb0


Resolution: 1.24→20.52 Å / SU ML: 0.0982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 3923 4.98 %
Rwork0.1677 74846 -
obs0.1687 78769 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.53 Å2
Refinement stepCycle: LAST / Resolution: 1.24→20.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 6 390 2367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532028
X-RAY DIFFRACTIONf_angle_d0.89712775
X-RAY DIFFRACTIONf_chiral_restr0.0778315
X-RAY DIFFRACTIONf_plane_restr0.0076363
X-RAY DIFFRACTIONf_dihedral_angle_d6.3054284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.26071090.26642444X-RAY DIFFRACTION92.3
1.26-1.270.23821220.25232542X-RAY DIFFRACTION96.03
1.27-1.290.25191250.22352617X-RAY DIFFRACTION98.14
1.29-1.310.29361250.2752571X-RAY DIFFRACTION96.8
1.31-1.320.23981600.1952599X-RAY DIFFRACTION99.21
1.32-1.340.19911320.18742636X-RAY DIFFRACTION99.53
1.34-1.360.20311300.18662645X-RAY DIFFRACTION99.82
1.36-1.390.18151530.17792652X-RAY DIFFRACTION99.89
1.39-1.410.21841380.16682632X-RAY DIFFRACTION100
1.41-1.440.19981480.16892629X-RAY DIFFRACTION99.96
1.44-1.460.17961450.17212672X-RAY DIFFRACTION99.89
1.46-1.490.21571400.16952651X-RAY DIFFRACTION99.89
1.49-1.530.17991390.16622654X-RAY DIFFRACTION100
1.53-1.560.17741550.16732661X-RAY DIFFRACTION100
1.56-1.60.18241470.1632658X-RAY DIFFRACTION100
1.6-1.640.18991300.17062701X-RAY DIFFRACTION99.96
1.64-1.690.19721200.17022704X-RAY DIFFRACTION100
1.69-1.750.1871260.16742672X-RAY DIFFRACTION100
1.75-1.810.18981510.17172686X-RAY DIFFRACTION100
1.81-1.880.18231510.16342674X-RAY DIFFRACTION100
1.88-1.970.17471310.16972697X-RAY DIFFRACTION99.93
1.97-2.070.16541460.16452694X-RAY DIFFRACTION100
2.07-2.20.18871620.16612721X-RAY DIFFRACTION100
2.2-2.370.19851430.16632713X-RAY DIFFRACTION100
2.37-2.610.16571390.17192749X-RAY DIFFRACTION100
2.61-2.990.19331550.17492759X-RAY DIFFRACTION100
2.99-3.760.15681440.15642840X-RAY DIFFRACTION100
3.76-20.520.20121570.15292973X-RAY DIFFRACTION99.49

+
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