[English] 日本語
Yorodumi
- PDB-7dzt: Cyrstal structure of PETase from Rhizobacter gummiphilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dzt
TitleCyrstal structure of PETase from Rhizobacter gummiphilus
ComponentsDLH domain-containing protein
KeywordsHYDROLASE / PET hydrolase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / PET hydrolase/cutinase-like domain-containing protein
Function and homology information
Biological speciesRhizobacter gummiphilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020M3A9I5037635 Korea, Republic Of
CitationJournal: J Hazard Mater / Year: 2021
Title: Implications for the PET decomposition mechanism through similarity and dissimilarity between PETases from Rhizobacter gummiphilus and Ideonella sakaiensis.
Authors: Sagong, H.Y. / Son, H.F. / Seo, H. / Hong, H. / Lee, D. / Kim, K.J.
History
DepositionJan 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DLH domain-containing protein
B: DLH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)57,0732
Polymers57,0732
Non-polymers00
Water2,252125
1
A: DLH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)28,5371
Polymers28,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DLH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)28,5371
Polymers28,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.267, 75.512, 200.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein DLH domain-containing protein


Mass: 28536.707 Da / Num. of mol.: 2 / Fragment: PET hydrolase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobacter gummiphilus (bacteria) / Strain: NS21 / Gene: A4W93_05950 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami-B / References: UniProt: A0A1W6L588
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.75 % / Mosaicity: 0.396 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 5 / Details: PEG 3350, Bis-tris

-
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 23, 2020
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 22066 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.049 / Rrim(I) all: 0.124 / Χ2: 7.128 / Net I/σ(I): 19.2 / Num. measured all: 144474
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.396.70.28910780.9660.1210.3144.823100
2.39-2.436.80.28611130.960.1190.314.745100
2.43-2.486.70.25710700.9620.1090.2794.867100
2.48-2.536.70.23210980.9680.0980.2525.052100
2.53-2.596.80.22110930.9740.0920.245.279100
2.59-2.656.70.19211130.9790.080.2085.403100
2.65-2.716.70.18111000.9790.0760.1965.916100
2.71-2.796.70.17810880.9760.0750.1946.337100
2.79-2.876.70.15611040.9840.0660.176.351100
2.87-2.966.70.1510900.9850.0630.1636.75100
2.96-3.076.70.13910990.9870.0580.1516.99100
3.07-3.196.70.13211290.9840.0560.1447.9100
3.19-3.336.70.11610900.9910.0490.1267.888100
3.33-3.516.60.11211040.9890.0470.1218.601100
3.51-3.736.60.10611180.9890.0450.1159.619100
3.73-4.026.50.09811180.9880.0420.1079.603100
4.02-4.426.40.09411250.9850.0410.10310.59599.9
4.42-5.066.30.08711260.9870.0390.0959.7798.8
5.06-6.376.20.08411470.990.0370.0928.37299.4
6.37-505.10.07710630.9890.0390.0868.56187.6

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 2.35→32.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.958 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.459 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 1084 4.9 %RANDOM
Rwork0.1995 ---
obs0.2027 20943 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.67 Å2 / Biso mean: 36.912 Å2 / Biso min: 3.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å2-0 Å2
2---1.37 Å20 Å2
3---2.42 Å2
Refinement stepCycle: final / Resolution: 2.35→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 0 125 4115
Biso mean---33.09 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173610
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6425570
X-RAY DIFFRACTIONr_angle_other_deg1.2591.5698406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5065532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82121.667192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45715614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2781526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
LS refinement shellResolution: 2.353→2.414 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 75 -
Rwork0.237 1467 -
all-1542 -
obs--94.95 %

+
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