[English] 日本語
Yorodumi
- PDB-8clq: Zearalenone lactonase of Streptomyces coelicoflavus mutant H286Y ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8clq
TitleZearalenone lactonase of Streptomyces coelicoflavus mutant H286Y in complex with hydrolyzed zearalenone
ComponentsHydrolase
KeywordsHYDROLASE / zearalenone / mycotoxin / lactonase / carboxylesterase / esterase / biodegradation / streptomyces coelicoflavus
Function / homologyChem-ZGR / :
Function and homology information
Biological speciesStreptomyces coelicoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPuehringer, D. / Mlynek, G.
Funding support Austria, Czech Republic, 5items
OrganizationGrant numberCountry
Christian Doppler ForschungsgesellschaftFA743017 Austria
Austrian Research Promotion AgencyLaura Bassi Center for Optimised Structural Studies Austria
Ministry of Education (MoE, Czech Republic)INBIO - CZ.02.1.01/0.0/0.0/16_026/0008451 Czech Republic
Ministry of Education (MoE, Czech Republic)RECETOX RI LM2018121 Czech Republic
Ministry of Education (MoE, Czech Republic)ELIXIR LM201813 Czech Republic
CitationJournal: Acs Catalysis / Year: 2024
Title: Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone.
Authors: Fruhauf, S. / Puhringer, D. / Thamhesl, M. / Fajtl, P. / Kunz-Vekiru, E. / Hobartner-Gussl, A. / Schatzmayr, G. / Adam, G. / Damborsky, J. / Djinovic-Carugo, K. / Prokop, Z. / Moll, W.D.
History
DepositionFeb 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydrolase
B: Hydrolase
C: Hydrolase
D: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,8028
Polymers139,4574
Non-polymers1,3464
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-0 kcal/mol
Surface area39960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.809, 129.867, 134.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Hydrolase


Mass: 34864.172 Da / Num. of mol.: 4 / Mutation: H286Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicoflavus (bacteria) / Gene: SMCF_1294 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H1Q8U7
#2: Chemical
ChemComp-ZGR / 2,4-dihydroxy-6-[(1E,10S)-10-hydroxy-6-oxoundec-1-en-1-yl]benzoic acid


Mass: 336.380 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C18H24O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.51 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Mg formate dihydrate 10.09% PEG 3350 (pH 6.9)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.53→46.77 Å / Num. obs: 174008 / % possible obs: 98.31 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2045 / Rpim(I) all: 0.08555 / Rrim(I) all: 0.222 / Net I/σ(I): 7.01
Reflection shellResolution: 1.53→1.585 Å / Redundancy: 5.8 % / Rmerge(I) obs: 4.244 / Mean I/σ(I) obs: 0.37 / Num. unique obs: 17042 / CC1/2: 0.0712 / CC star: 0.365 / Rpim(I) all: 1.902 / Rrim(I) all: 4.664 / % possible all: 85.93

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4489refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→46.77 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 1970 1.15 %
Rwork0.1975 --
obs0.1978 171289 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9457 0 96 629 10182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049863
X-RAY DIFFRACTIONf_angle_d0.73613450
X-RAY DIFFRACTIONf_dihedral_angle_d9.261381
X-RAY DIFFRACTIONf_chiral_restr0.0441403
X-RAY DIFFRACTIONf_plane_restr0.0061780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.40841190.409510019X-RAY DIFFRACTION82
1.57-1.610.39921290.395311743X-RAY DIFFRACTION96
1.61-1.660.37181410.375711976X-RAY DIFFRACTION99
1.66-1.710.38471370.356512194X-RAY DIFFRACTION100
1.71-1.770.33951470.331112140X-RAY DIFFRACTION100
1.77-1.840.30911480.307312193X-RAY DIFFRACTION100
1.84-1.930.28181370.271212255X-RAY DIFFRACTION100
1.93-2.030.26831470.227812232X-RAY DIFFRACTION100
2.03-2.160.20971400.203412253X-RAY DIFFRACTION100
2.16-2.320.20311410.183212295X-RAY DIFFRACTION100
2.32-2.560.21431460.171412315X-RAY DIFFRACTION100
2.56-2.930.1971400.162212393X-RAY DIFFRACTION100
2.93-3.690.18361460.148812464X-RAY DIFFRACTION100
3.69-46.770.16271520.157912847X-RAY DIFFRACTION100

+
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