[English] 日本語
Yorodumi
- PDB-5o4l: Crystal structure of P450 CYP121 in complex with compound 6a. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o4l
TitleCrystal structure of P450 CYP121 in complex with compound 6a.
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / Cytochrome P450 Redox Inhibitor
Function / homology
Function and homology information


mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / 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
Chem-9KB / PROTOPORPHYRIN IX CONTAINING FE / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsLevy, C.W.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Novel Aryl Substituted Pyrazoles as Small Molecule Inhibitors of Cytochrome P450 CYP121A1: Synthesis and Antimycobacterial Evaluation.
Authors: Taban, I.M. / Elshihawy, H.E.A.E. / Torun, B. / Zucchini, B. / Williamson, C.J. / Altuwairigi, D. / Ngu, A.S.T. / McLean, K.J. / Levy, C.W. / Sood, S. / Marino, L.B. / Munro, A.W. / de ...Authors: Taban, I.M. / Elshihawy, H.E.A.E. / Torun, B. / Zucchini, B. / Williamson, C.J. / Altuwairigi, D. / Ngu, A.S.T. / McLean, K.J. / Levy, C.W. / Sood, S. / Marino, L.B. / Munro, A.W. / de Carvalho, L.P.S. / Simons, C.
History
DepositionMay 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3354
Polymers43,3061
Non-polymers1,0293
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-45 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.530, 77.530, 264.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-562-

HOH

21A-800-

HOH

-
Components

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43305.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Gene: cyp121, MT2336 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP6, EC: 1.14.21.9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-9KB / 1-[(4-fluorophenyl)methyl]-4-(3-imidazol-1-ylpropyl)piperazin-2-one


Mass: 316.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21FN4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.5 to 2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5 to 6.15
PH range: 5.5 - 6.15 / Temp details: Cold Room

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.64→67.14 Å / Num. obs: 58784 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.99 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.041 / Net I/σ(I): 12.5
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 20 % / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5714 / CC1/2: 0.486 / Rpim(I) all: 0.451 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Inhouse

Resolution: 1.64→67.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.339 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19048 2000 3.4 %RANDOM
Rwork0.16263 ---
obs0.16358 56784 99.85 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 23.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å2-0 Å2
2---0.14 Å2-0 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.64→67.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 71 402 3504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193265
X-RAY DIFFRACTIONr_bond_other_d0.0020.023143
X-RAY DIFFRACTIONr_angle_refined_deg1.6822.0064464
X-RAY DIFFRACTIONr_angle_other_deg1.512.9977280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.30523.022139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85415548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4371533
X-RAY DIFFRACTIONr_chiral_restr0.1090.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213610
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02662
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_it1.8931.1891593
X-RAY DIFFRACTIONr_mcbond_other1.8911.1881592
X-RAY DIFFRACTIONr_mcangle_it2.4841.7721995
X-RAY DIFFRACTIONr_mcangle_other2.4851.7721996
X-RAY DIFFRACTIONr_scbond_it4.9111.7241672
X-RAY DIFFRACTIONr_scbond_other4.911.7251673
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7352.3842466
X-RAY DIFFRACTIONr_long_range_B_refined8.06617.0093763
X-RAY DIFFRACTIONr_long_range_B_other7.94616.073663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 144 -
Rwork0.317 4099 -
obs--99.51 %
Refinement TLS params.Method: refined / Origin x: -6.23 Å / Origin y: 21.524 Å / Origin z: 11.47 Å
111213212223313233
T0.1004 Å2-0.0063 Å20.0044 Å2-0.0334 Å2-0.0011 Å2--0.0027 Å2
L0.46 °20.0445 °2-0.0554 °2-0.4264 °20.0041 °2--0.7954 °2
S0.0196 Å °-0.0068 Å °0.0295 Å °-0.0059 Å °0.0065 Å °-0.0008 Å °-0.1629 Å °-0.0204 Å °-0.0261 Å °

+
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