[English] 日本語
Yorodumi
- PDB-3p99: Sterol 14alpha-demethylase (CYP51) from Trypanosoma brucei in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p99
TitleSterol 14alpha-demethylase (CYP51) from Trypanosoma brucei in complex with delta7-14alpha-methylene-cyclopropyl-dihydrolanosterol
ComponentsSterol 14-alpha-demethylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 fold/sterol 14-alpha demethylase / CYP51 / monooxygenase / hemoprotein / sterol biosynthesis / cytochrome P450 reductase (CPR) / endoplasmic reticulum / membrane
Function / homology
Function and homology information


membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / nuclear envelope / iron ion binding / heme binding / endoplasmic reticulum
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 / Chem-LNP / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLepesheva, G.I. / Hargrove, T.Y. / Waterman, M.R. / Wawrzak, Z.
CitationJournal: J.Lipid Res. / Year: 2012
Title: Structural complex of sterol 14alpha-demethylase (CYP51) with 14alpha-methylenecyclopropyl-delta7-24, 25-dihydrolanosterol
Authors: Hargrove, T.Y. / Wawrzak, Z. / Liu, J. / Waterman, M.R. / Nes, W.D. / Lepesheva, G.I.
History
DepositionOct 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)209,02712
Polymers204,6944
Non-polymers4,3338
Water90150
1
A: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers51,1731
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.610, 80.570, 115.800
Angle α, β, γ (deg.)107.93, 102.43, 99.57
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Sterol 14-alpha-demethylase


Mass: 51173.395 Da / Num. of mol.: 4 / Fragment: unp residues 29-481 / Mutation: G29P, K30T, L31D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: CYP51, Tb11.02.4080 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q385E8, 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-LNP / (3alpha,9beta,10alpha,13alpha)-30-cyclopropylidenelanost-7-en-3-ol


Mass: 466.781 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H54O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 297 K / pH: 7.2
Details: PEG 3350, POTASSIUM PHOSPHATE; n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE, delta7-14alpha-methylene-cyclopropyl-dihydrolanosterol, pH 7.2, VAPOR DIFFUSION, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010 / Details: BE LENSES/DIAMOND LAUE MONO
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→29.39 Å / Num. obs: 37941 / % possible obs: 97.6 % / Observed criterion σ(I): 2.6 / Redundancy: 3.8 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.068 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.94 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.55 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G1Q

3g1q


Resolution: 3→29.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 51.98 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27144 1894 5 %RANDOM
Rwork0.22313 ---
obs0.2256 36047 97.78 %-
all-36857 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.529 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20.35 Å20.57 Å2
2--1.4 Å21.91 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 3→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14197 0 308 50 14555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02214876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8942.02220220
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.03151783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06123.231650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.252152589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.19415120
X-RAY DIFFRACTIONr_chiral_restr0.0490.22216
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02111164
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7541.58959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.413214533
X-RAY DIFFRACTIONr_scbond_it2.48935917
X-RAY DIFFRACTIONr_scangle_it4.0124.55675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 145 -
Rwork0.248 2633 -
obs--97.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.42890.23230.16582.79380.87952.93770.11870.0339-0.0471-0.2087-0.0925-0.2296-0.2093-0.0971-0.02610.20280.0940.07020.2880.11470.257618.229625.0856-36.6539
21.97120.66950.66473.53581.86215.10050.1846-0.0739-0.0440.37380.2771-0.3563-0.25960.2332-0.46180.28390.06030.07940.19810.01710.359714.4053-35.216914.4858
33.3107-0.08950.06382.4319-0.01062.1435-0.0845-0.04410.06440.27560.00770.1073-0.1270.1840.07680.2475-0.04060.04610.11080.01680.063313.31955.569620.9986
43.9954-0.54360.40495.9863-0.78982.6196-0.0709-0.00740.26790.106-0.0902-0.5018-0.25240.28950.1610.0418-0.0313-0.06780.20060.03430.194132.215-13.5139-31.4347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 476
2X-RAY DIFFRACTION1A482 - 490
3X-RAY DIFFRACTION1A3 - 28
4X-RAY DIFFRACTION1A483 - 491
5X-RAY DIFFRACTION2B29 - 476
6X-RAY DIFFRACTION2B482 - 490
7X-RAY DIFFRACTION2B2 - 22
8X-RAY DIFFRACTION2B483 - 487
9X-RAY DIFFRACTION3C29 - 476
10X-RAY DIFFRACTION3C482 - 490
11X-RAY DIFFRACTION3C13 - 27
12X-RAY DIFFRACTION3C483 - 487
13X-RAY DIFFRACTION4D29 - 476
14X-RAY DIFFRACTION4D482 - 490
15X-RAY DIFFRACTION4D1 - 26
16X-RAY DIFFRACTION4D483 - 486

+
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