[English] 日本語
Yorodumi
- PDB-7xtt: The structure of engineered TfCut S130A in complex with MHET -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xtt
TitleThe structure of engineered TfCut S130A in complex with MHET
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / PET hydrolase / PBAT hydrolase / enzyme engineering / cutinase
Function / homology4-(2-hydroxyethyloxycarbonyl)benzoic acid
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsYang, Y. / Jiang, P.C. / Huang, J.W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870790 China
National Natural Science Foundation of China (NSFC)31971205 China
National Natural Science Foundation of China (NSFC)32101016 China
CitationJournal: Nat Commun / Year: 2023
Title: Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases.
Authors: Yang, Y. / Min, J. / Xue, T. / Jiang, P. / Liu, X. / Peng, R. / Huang, J.W. / Qu, Y. / Li, X. / Ma, N. / Tsai, F.C. / Dai, L. / Zhang, Q. / Liu, Y. / Chen, C.C. / Guo, R.T.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha/beta hydrolase
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0889
Polymers56,5492
Non-polymers5387
Water12,304683
1
A: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3372
Polymers28,2751
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7517
Polymers28,2751
Non-polymers4766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.838, 41.903, 80.868
Angle α, β, γ (deg.)90.000, 92.110, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein alpha/beta hydrolase / Cutinase


Mass: 28274.725 Da / Num. of mol.: 2 / Mutation: S130A,H184S,F188I
Source method: isolated from a genetically manipulated source
Details: GB:PZN61876.1 / Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: cut-2.KW3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: cutinase

-
Non-polymers , 5 types, 690 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 30% W/V PEG8000; 0.2 M Ammonium sulfate; 0.1 M Sodium cacodylate 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Dec 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.82→32.62 Å / Num. obs: 75313 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.0337 / Net I/σ(I): 38.62
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.1047 / Mean I/σ(I) obs: 8.95 / Num. unique obs: 1821 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
SADABSdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zoa

5zoa


Resolution: 1.82→32.62 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.173 3782 5.02 %
Rwork0.1361 71531 -
obs0.138 75313 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.6 Å2 / Biso mean: 12.2804 Å2 / Biso min: 0.1 Å2
Refinement stepCycle: final / Resolution: 1.82→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 34 683 4685
Biso mean--19.77 22.14 -
Num. residues----523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.840.22621190.16022444256391
1.84-1.870.20551430.14832510265393
1.87-1.890.20761380.15482565270393
1.89-1.920.20011350.14762505264093
1.92-1.950.20771370.14772533267094
1.95-1.980.19081590.13942619277895
1.98-2.010.19481410.13932561270295
2.01-2.050.1721350.12952596273196
2.05-2.080.16251560.13312636279296
2.08-2.120.18471210.13492629275097
2.12-2.170.20261470.13262690283797
2.17-2.210.181380.13252629276797
2.21-2.270.17351310.13422639277098
2.27-2.320.19161440.13162738288299
2.32-2.380.16941380.13052679281799
2.38-2.450.17311470.139827652912100
2.45-2.530.19211450.137927162861100
2.53-2.620.1791320.139227162848100
2.62-2.730.17161500.139626742824100
2.73-2.850.19651420.140127322874100
2.85-30.19931320.146328112943100
3-3.190.16841400.139626432783100
3.19-3.440.15571540.134927342888100
3.44-3.780.1441460.128227282874100
3.78-4.330.13021360.112127002836100
4.33-5.450.14481400.12627162856100
5.45-32.620.16831360.15772623275996

+
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