[English] 日本語
Yorodumi
- PDB-6fmo: Crystal structure of the substrate (obtusifoliol)-bound and ligan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fmo
TitleCrystal structure of the substrate (obtusifoliol)-bound and ligand-free I105F mutant of sterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi
ComponentsSterol 14alpha-demethylase
KeywordsPROTEIN BINDING / sterol biosynthesis / CYP51 / OXIDOREDUCTASE / MONOOXYGENASE / SUBSTRATE BINDING
Function / homology
Function and homology information


sterol 14alpha-demethylase / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / methyltransferase 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
Obtusifoliol / PROTOPORPHYRIN IX CONTAINING FE / Sterol 14alpha-demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Lepesheva, G.I.
Funding support1items
OrganizationGrant numberCountry
GM 067871
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Binding of a physiological substrate causes large-scale conformational reorganization in cytochrome P450 51.
Authors: Hargrove, T.Y. / Wawrzak, Z. / Fisher, P.M. / Child, S.A. / Nes, W.D. / Guengerich, F.P. / Waterman, M.R. / Lepesheva, G.I.
History
DepositionFeb 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sterol 14alpha-demethylase
B: Sterol 14alpha-demethylase
C: Sterol 14alpha-demethylase
D: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,05111
Polymers221,3054
Non-polymers3,7467
Water905
1
A: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3693
Polymers55,3261
Non-polymers1,0432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3693
Polymers55,3261
Non-polymers1,0432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3693
Polymers55,3261
Non-polymers1,0432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9432
Polymers55,3261
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.310, 154.310, 178.876
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 31 - 478 / Label seq-ID: 31 - 478

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Sterol 14alpha-demethylase


Mass: 55326.188 Da / Num. of mol.: 4 / Mutation: I105F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: CYP51A / Production host: Escherichia coli (E. coli) / Variant (production host): HMS174
References: UniProt: M1FYE4, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DVE / Obtusifoliol


Mass: 426.717 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C30H50O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Obtusifoliol, PEG 4000, potassium phosphate, sodium chloride
PH range: 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2017 / Details: focusing mirrors
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 3.18→133.64 Å / Num. obs: 38484 / % possible obs: 99.3 % / Redundancy: 6.2 % / CC1/2: 0.386 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.6
Reflection shellResolution: 3.18→3.27 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2990 / Rpim(I) all: 0.697 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ck8

4ck8


Resolution: 3.18→133.64 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / SU B: 33.432 / SU ML: 0.533 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29289 2141 5.3 %RANDOM
Rwork0.25988 ---
obs0.26162 38484 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 156.443 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0.35 Å2-0 Å2
2---0.71 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 3.18→133.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14175 0 265 5 14445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01914986
X-RAY DIFFRACTIONr_bond_other_d0.0050.0214186
X-RAY DIFFRACTIONr_angle_refined_deg0.8461.99120345
X-RAY DIFFRACTIONr_angle_other_deg0.6773.00332886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96651788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39323.432676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.248152628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.14715116
X-RAY DIFFRACTIONr_chiral_restr0.050.22199
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02116418
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023094
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.115.6677164
X-RAY DIFFRACTIONr_mcbond_other13.115.6667163
X-RAY DIFFRACTIONr_mcangle_it20.23523.4818948
X-RAY DIFFRACTIONr_mcangle_other20.23523.4828949
X-RAY DIFFRACTIONr_scbond_it11.58616.0257822
X-RAY DIFFRACTIONr_scbond_other11.58316.0267820
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.45123.74811397
X-RAY DIFFRACTIONr_long_range_B_refined26.84917781
X-RAY DIFFRACTIONr_long_range_B_other26.8517780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A295740.06
12B295740.06
21A291040.08
22C291040.08
31A277760.12
32D277760.12
41B294780.06
42C294780.06
51B277220.12
52D277220.12
61C276140.12
62D276140.12
LS refinement shellResolution: 3.184→3.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 147 -
Rwork0.366 2805 -
obs--98.53 %

+
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