[English] 日本語
Yorodumi
- PDB-5ead: Saccharomyces cerevisiae CYP51 complexed with the plant pathogen ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ead
TitleSaccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor S-desthio-prothioconazole
ComponentsLanosterol 14-alpha demethylase
KeywordsOxidoreductase/Oxidoreducatse inhibitor / CYP51 / S-desthio-prothioconazole / oxidoreductase-oxidoreductase inhibitor complex / Oxidoreductase-Oxidoreducatse inhibitor complex
Function / homology
Function and homology information


sterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / methyltransferase activity / monooxygenase activity / methylation / iron ion binding / heme binding / membrane
Similarity search - Function
Cytochrome P450, E-class, group IV / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-5L9 / PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsTyndall, J.D.A. / Sabherwal, M. / Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Woods, M.V. / Monk, B.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Bayer CropScience Germany
Citation
Journal: PLoS ONE / Year: 2016
Title: Structural and Functional Elucidation of Yeast Lanosterol 14 alpha-Demethylase in Complex with Agrochemical Antifungals.
Authors: Tyndall, J.D. / Sabherwal, M. / Sagatova, A.A. / Keniya, M.V. / Negroni, J. / Wilson, R.K. / Woods, M.A. / Tietjen, K. / Monk, B.C.
#1: Journal: Antimicrob. Agents Chemother. / Year: 2015
Title: Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Monk, B.C. / Tyndall, J.D.
History
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8143
Polymers61,8851
Non-polymers9292
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-26 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.270, 67.180, 80.910
Angle α, β, γ (deg.)90.000, 99.090, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61885.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SDE is the small molecule S-desthio-prothioconazole
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZSR0
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-5L9 / (2~{S})-2-(1-chloranylcyclopropyl)-1-(2-chlorophenyl)-3-(1,2,4-triazol-1-yl)propan-2-ol / S-desthio-prothioconazole


Mass: 312.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15Cl2N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: 45% PEG 400, 0.1M GLYCINE / PH range: 9.4-9.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→30.267 Å / Num. obs: 56012 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.04 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.06 / Net I/σ(I): 5.8 / Num. measured all: 219677 / Scaling rejects: 167
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.053.90.731.41620641310.810.4299.4
8.94-79.893.70.0413.223306310.9970.02393

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å30.27 Å
Translation7.76 Å30.27 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.7data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2→30.267 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 2820 5.04 %
Rwork0.1945 103902 -
obs0.196 55946 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.53 Å2 / Biso mean: 43.7354 Å2 / Biso min: 20.89 Å2
Refinement stepCycle: final / Resolution: 2→30.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 63 152 4492
Biso mean--28.84 41.05 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094476
X-RAY DIFFRACTIONf_angle_d1.1016083
X-RAY DIFFRACTIONf_chiral_restr0.045643
X-RAY DIFFRACTIONf_plane_restr0.005780
X-RAY DIFFRACTIONf_dihedral_angle_d14.3831662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02280.33371890.31523582377199
2.0228-2.04660.37031760.31063362353899
2.0466-2.07150.34551650.29933492365799
2.0715-2.09770.32551790.28353455363499
2.0977-2.12530.25252010.275934403641100
2.1253-2.15440.32491930.26623515370899
2.1544-2.18520.28581920.25013425361799
2.1852-2.21780.27811960.246234193615100
2.2178-2.25240.2981890.25143449363899
2.2524-2.28940.24911750.24783495367099
2.2894-2.32880.30632070.21534083615100
2.3288-2.37120.211630.20963493365699
2.3712-2.41670.23671540.206734823636100
2.4167-2.46610.22461890.195835003689100
2.4661-2.51960.21311960.199434643660100
2.5196-2.57820.21841590.204334873646100
2.5782-2.64270.28371600.197734393599100
2.6427-2.71410.28082050.20134833688100
2.7141-2.79390.21491500.19643520367099
2.7939-2.8840.2051730.186134653638100
2.884-2.9870.21942140.175733983612100
2.987-3.10650.17772060.191334963702100
3.1065-3.24770.24711700.201234703640100
3.2477-3.41870.25661920.196834663658100
3.4187-3.63260.19891710.187234773648100
3.6326-3.91250.20242070.170634573664100
3.9125-4.30520.19862080.164534523660100
4.3052-4.92590.16591630.14873463362699
4.9259-6.19740.20052070.18433418362599
6.1974-30.270.20671650.17773430359598

+
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