[English] 日本語
Yorodumi
- PDB-5esi: Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5esi
TitleSaccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) G73W mutant
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / CYP51
Function / homology
Function and homology information


sterol 14alpha-demethylase / 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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSagatova, A. / Keniya, M.V. / Wilson, R. / Sabherwal, M. / Tyndall, J.D.A. / Monk, B.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
Marsden Fund New Zealand
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2018
Title: Impact of Homologous Resistance Mutations from Pathogenic Yeast on Saccharomyces cerevisiae Lanosterol 14 alpha-Demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Tyndall, J.D.A. / Monk, B.C.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2014
Title: Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer.
Authors: Monk, B.C. / Tomasiak, T.M. / Keniya, M.V. / Huschmann, F.U. / Tyndall, J.D.A. / O'Connell III, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M.
#2: 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
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 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: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6312
Polymers62,0141
Non-polymers6161
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-27 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.900, 67.050, 80.980
Angle α, β, γ (deg.)90.00, 99.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 62014.371 Da / Num. of mol.: 1 / Mutation: G73W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2delta / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG-400 45%, 0.1 M glycine / PH range: 9.3-9.5

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→60.95 Å / Num. obs: 47947 / % possible obs: 98 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / % possible all: 92.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.1→33.66 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 2424 5.06 %
Rwork0.1895 --
obs0.1914 47908 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 43 185 4525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084468
X-RAY DIFFRACTIONf_angle_d1.0646069
X-RAY DIFFRACTIONf_dihedral_angle_d13.3991644
X-RAY DIFFRACTIONf_chiral_restr0.042642
X-RAY DIFFRACTIONf_plane_restr0.005767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14290.29271440.26742472X-RAY DIFFRACTION92
2.1429-2.18940.28781300.24382552X-RAY DIFFRACTION94
2.1894-2.24040.28681560.23512575X-RAY DIFFRACTION95
2.2404-2.29640.25681250.22942544X-RAY DIFFRACTION95
2.2964-2.35850.28151500.21062622X-RAY DIFFRACTION97
2.3585-2.42780.2671190.20772658X-RAY DIFFRACTION98
2.4278-2.50620.23341500.19312673X-RAY DIFFRACTION98
2.5062-2.59570.20891390.19862725X-RAY DIFFRACTION99
2.5957-2.69960.26551300.19352728X-RAY DIFFRACTION100
2.6996-2.82240.291310.19972724X-RAY DIFFRACTION100
2.8224-2.97110.24061570.19562717X-RAY DIFFRACTION100
2.9711-3.15710.22041500.19122724X-RAY DIFFRACTION100
3.1571-3.40070.23071500.19482719X-RAY DIFFRACTION100
3.4007-3.74250.20551380.17782753X-RAY DIFFRACTION100
3.7425-4.28310.21071690.17312711X-RAY DIFFRACTION100
4.2831-5.39270.1931390.15932774X-RAY DIFFRACTION100
5.3927-33.66470.19941470.18612813X-RAY DIFFRACTION99

+
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