[English] 日本語
Yorodumi
- PDB-2wuz: X-ray structure of CYP51 from Trypanosoma cruzi in complex with f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wuz
TitleX-ray structure of CYP51 from Trypanosoma cruzi in complex with fluconazole in alternative conformation
ComponentsLANOSTEROL 14-ALPHA-DEMETHYLASE, PUTATIVE
KeywordsOXIDOREDUCTASE / METHYLTRANSFERASE / P450 / IRON / CYP51 / METAL-BINDING / ERGOSTEROL BIOSYNTHESIS
Function / homology
Function and homology information


sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / 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 / Chem-TPF / Sterol 14-alpha demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChen, C.-K. / Leung, S.S.F. / Guilbert, C. / Jacobson, M. / McKerrow, J.H. / Podust, L.M.
CitationJournal: Plos Negl Trop Dis / Year: 2010
Title: Structural Characterization of Cyp51 from Trypanosoma Cruzi and Trypanosoma Brucei Bound to the Antifungal Drugs Posaconazole and Fluconazole
Authors: Chen, C.-K. / Leung, S.S.F. / Guilbert, C. / Jacobson, M. / Mckerrow, J.H. / Podust, L.M.
History
DepositionOct 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _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, PUTATIVE
B: LANOSTEROL 14-ALPHA-DEMETHYLASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0876
Polymers108,2422
Non-polymers1,8464
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-64.1 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.858, 92.574, 78.277
Angle α, β, γ (deg.)90.00, 102.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 30 - 475 / Label seq-ID: 16 - 461

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.99986, 0.00118, 0.01678), (-0.00103, -0.99996, 0.00896), (0.01679, 0.00894, 0.99982)
Vector: 37.33375, -15.76784, -0.36569)

-
Components

#1: Protein LANOSTEROL 14-ALPHA-DEMETHYLASE, PUTATIVE / STEROL 14 ALPHA-DEMETHYLASE / CYP51


Mass: 54120.766 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q5I4E1, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TPF / 2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL / FLUCONAZOLE / ALPHA-(2,4-DIFLUOROPHENYL)-ALPHA-(1H-1,2,4-TRIAZOLE-1-YLMETHYL)-1H-1,2,4-TRIAZOLE-1-ETHANOL / ELAZOR / TRIFLUCAN / BIOZOLENE / Fluconazole


Mass: 306.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12F2N6O / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN THE HEME FE AND CYS422 FLUCONAZOLE ...PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN THE HEME FE AND CYS422 FLUCONAZOLE (TPF): COORDINATION BOND BETWEEN THE HEME FE AND FLUCONAZOLE
Sequence detailsTHE FIRST 21 RESIDUES UPSTREAM OF K22 WERE REPLACED WITH THE FRAGMENT MAKKKKK AT THE N-TERMINUS. ...THE FIRST 21 RESIDUES UPSTREAM OF K22 WERE REPLACED WITH THE FRAGMENT MAKKKKK AT THE N-TERMINUS. HIS6-TAG WAS INTRODUCED AT THE C-TERMINUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 6 / Details: 40% POLYPROPYLENE GLYCOL 400, 0.1 TRIS-HCL, PH=6.0

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 21, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.35→76.5 Å / Num. obs: 40838 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 70.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WV2

2wv2


Resolution: 2.35→76.53 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 19.542 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. SIDE CHAINS NOT VISIBLE IN THE DENSITY WAS MODELED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.27476 2046 5 %RANDOM
Rwork0.21739 ---
obs0.22028 38792 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.638 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.48 Å2
2---1.32 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.35→76.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 130 176 7265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8912.019948
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51523.183311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.932151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1711555
X-RAY DIFFRACTIONr_chiral_restr0.1140.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215564
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_it0.8411.54472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4527224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32432842
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5234.52724
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.53437314
X-RAY DIFFRACTIONr_sphericity_free8.2883179
X-RAY DIFFRACTIONr_sphericity_bonded2.12837124
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1684tight positional0.060.05
2B1684tight positional0.060.05
1A1628medium positional0.10.5
2B1628medium positional0.10.5
1A1684tight thermal0.10.5
2B1684tight thermal0.10.5
1A1628medium thermal0.12
2B1628medium thermal0.12
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 99 -
Rwork0.244 1964 -
obs--64.01 %
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)
10.7008-0.3741-0.29242.5695-0.71.18140.0494-0.08640.05140.5103-0.1049-0.22110.0030.21420.05560.1901-0.0044-0.04930.10110.05090.094339.017-21.72116.287
20.9391-0.70140.18412.0865-0.31331.62210.13-0.0112-0.22990.0891-0.13270.02040.16930.11350.00270.09020.0299-0.02020.06310.04810.095633.498-28.1978.555
30.4559-0.11790.36432.10160.35781.29990.0034-0.06340.02870.4076-0.04680.2513-0.0688-0.34610.04340.11120.03230.05340.1328-0.03290.1065-1.3196.36816.412
41.0693-0.50620.60491.89530.18352.37390.1080.04280.23040.1169-0.04750.0036-0.16-0.1828-0.06060.07770.04770.04270.0633-0.01230.13343.96212.4359.224
51.1423-0.19390.31332.97120.43231.9550.13140.28820.0865-0.4125-0.2628-0.1849-0.02620.27370.13150.07910.07680.05290.13910.06550.104136.499-18.283-2.165
60.7663-0.17970.0351.7608-0.26071.0657-0.0011-0.18030.14770.4001-0.1060.0446-0.1044-0.05510.10710.1586-0.02290.01940.12480.00040.090929.308-7.63117.493
70.8978-0.27370.20512.4235-0.62041.84120.13920.1475-0.0699-0.2209-0.15330.16110.0297-0.28340.01410.06850.0597-0.04310.1266-0.03960.07211.1872.576-2.015
81.0030.0986-0.09991.88780.36751.4361-0.0232-0.0895-0.13190.3922-0.1164-0.03440.2471-0.13690.13970.1489-0.0131-0.02760.0814-0.0090.07238.488-7.70517.68
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A257 - 362
2X-RAY DIFFRACTION2A363 - 476
3X-RAY DIFFRACTION3B260 - 362
4X-RAY DIFFRACTION4B363 - 480
5X-RAY DIFFRACTION5A27 - 150
6X-RAY DIFFRACTION6A151 - 250
7X-RAY DIFFRACTION7B28 - 150
8X-RAY DIFFRACTION8B151 - 250

+
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