[English] 日本語
Yorodumi
- PDB-4lxj: Saccharomyces cerevisiae lanosterol 14-alpha demethylase with lan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lxj
TitleSaccharomyces cerevisiae lanosterol 14-alpha demethylase with lanosterol bound
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / Cytochrome p450
Function / homology
Function and homology information


Endogenous sterols / Cholesterol biosynthesis / ergosterol biosynthetic process / sterol 14alpha-demethylase / sterol 14-demethylase activity / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum
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
PROTOPORPHYRIN IX CONTAINING FE / LANOSTEROL / OXYGEN MOLECULE / Lanosterol 14-alpha demethylase CYP51
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMonk, 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. / Rodriguez, A. / Finer-Moore, J. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / 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. / O'Connell, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Structure summary
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)62,5464
Polymers61,4711
Non-polymers1,0753
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.213, 67.005, 80.378
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lanosterol 14-alpha demethylase / CYPLI / Cytochrome P450 51 / Cytochrome P450-14DM / Cytochrome P450-LIA1 / Sterol 14-alpha demethylase


Mass: 61470.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERG11, CYP51, YHR007C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10614, sterol 14alpha-demethylase
#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-LAN / LANOSTEROL


Mass: 426.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50O
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9
Details: 49% PEG 400, 100mM Glycine pH 9.0, VAPOR DIFFUSION, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Khozu double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 64791 / Num. obs: 62523 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.2 % / Rsym value: 0.531 / % possible all: 72.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LD6

3ld6


Resolution: 1.9→29.327 Å / SU ML: 0.2 / σ(F): 1.38 / Phase error: 26.16 / Stereochemistry target values: ML
Details: VISUAL INSPECTION OF THE ELECTRON DENSITY MAPS AND A HIGH REAL SPACE R-FACTOR INDICATED THE NEED FOR CONSIDERABLE CARE IN PLACEMENT OF THE LIGAND IN THE LANOSTEROL CO-STRUCTURE. MINIMALLY ...Details: VISUAL INSPECTION OF THE ELECTRON DENSITY MAPS AND A HIGH REAL SPACE R-FACTOR INDICATED THE NEED FOR CONSIDERABLE CARE IN PLACEMENT OF THE LIGAND IN THE LANOSTEROL CO-STRUCTURE. MINIMALLY BIASED FO-FC ELECTRON DENSITY OMIT MAPS, CALCULATED WITH LANOSTEROL OMITTED TO CORRECTLY PLACE THE LANOSTEROL, RESULTED IN A REASONABLE CORRELATION COEFFICIENT (0.813).
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3117 4.99 %Random
Rwork0.195 ---
obs0.1966 62492 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 76 182 4545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114492
X-RAY DIFFRACTIONf_angle_d1.4236108
X-RAY DIFFRACTIONf_dihedral_angle_d15.0581666
X-RAY DIFFRACTIONf_chiral_restr0.086649
X-RAY DIFFRACTIONf_plane_restr0.006769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92970.37711030.31761998X-RAY DIFFRACTION73
1.9297-1.96130.34161080.31192235X-RAY DIFFRACTION79
1.9613-1.99510.34191140.29832456X-RAY DIFFRACTION89
1.9951-2.03140.27291370.27222693X-RAY DIFFRACTION96
2.0314-2.07050.31211360.25682752X-RAY DIFFRACTION98
2.0705-2.11270.27111580.24282760X-RAY DIFFRACTION99
2.1127-2.15870.23731460.23012748X-RAY DIFFRACTION99
2.1587-2.20880.24741600.20932720X-RAY DIFFRACTION99
2.2088-2.26410.23671490.2092761X-RAY DIFFRACTION99
2.2641-2.32530.23641550.20312760X-RAY DIFFRACTION99
2.3253-2.39370.25271180.19542789X-RAY DIFFRACTION99
2.3937-2.47090.22591510.18832753X-RAY DIFFRACTION99
2.4709-2.55910.20561420.1882791X-RAY DIFFRACTION99
2.5591-2.66150.23761380.18442762X-RAY DIFFRACTION100
2.6615-2.78260.2391370.1912815X-RAY DIFFRACTION100
2.7826-2.92920.22971450.18962767X-RAY DIFFRACTION99
2.9292-3.11250.23591610.18972764X-RAY DIFFRACTION99
3.1125-3.35250.2171500.20052800X-RAY DIFFRACTION100
3.3525-3.68930.22431400.18112814X-RAY DIFFRACTION100
3.6893-4.22180.2241710.17642787X-RAY DIFFRACTION100
4.2218-5.31380.19141490.17092813X-RAY DIFFRACTION100
5.3138-29.33010.2161490.2012837X-RAY DIFFRACTION98

+
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