[English] 日本語
Yorodumi
- PDB-2jjp: Structure of cytochrome P450 EryK in complex with inhibitor ketoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jjp
TitleStructure of cytochrome P450 EryK in complex with inhibitor ketoconazole (KC)
ComponentsCYTOCHROME P450 113A1
KeywordsOXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / ANTIBIOTIC BIOSYNTHESIS / TIE-ROD MECHANISM OF ACTION / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


erythromycin 12-hydroxylase / macrolide biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / NADP binding / iron ion binding / heme binding
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-KLN / Erythromycin C-12 hydroxylase
Similarity search - Component
Biological speciesSACCHAROPOLYSPORA ERYTHRAEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSavino, C. / Sciara, G. / Miele, A.E. / Kendrew, S.G. / Vallone, B.
CitationJournal: Biochemistry / Year: 2010
Title: Azole Drugs Trap Cytochrome P450 Eryk in Alternative Conformational States.
Authors: Montemiglio, L.C. / Gianni, S. / Vallone, B. / Savino, C.
History
DepositionApr 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 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 / struct_conn / 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 / _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_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: CYTOCHROME P450 113A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6875
Polymers45,3471
Non-polymers1,3404
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.243, 68.038, 57.687
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CYTOCHROME P450 113A1 / ERYTHROMYCIN B/D C-12 HYDROXYLASE / CYTOCROME P450 CYP113A1


Mass: 45347.031 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Strain: NRRL 23338 / Description: CDNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR
References: UniProt: P48635, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-KLN / 1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL]METHOXY}PHENYL)PIPERAZINE


Mass: 531.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28Cl2N4O4 / Comment: inhibitor*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO LEU ENGINEERED RESIDUE IN CHAIN A, PHE 330 TO LEU

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 2.0M AMMONIUM SULHATE, 0.1M BIS-TRIS PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 25326 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 12.7 / % possible all: 85.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJN

2jjn


Resolution: 2.1→56.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.695 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COORDINATE START FROM A.A. 15 BECAUSE THERE WAS NOT ELECTRON DENSITY FOR PREVIOUS RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1109 5.1 %RANDOM
Rwork0.195 ---
obs0.199 20602 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å2-0.79 Å2
2--4.54 Å20 Å2
3----2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 89 229 3397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6112.0254545
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52723.832167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05815529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.981534
X-RAY DIFFRACTIONr_chiral_restr0.1010.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.21684
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22229
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0961.52046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77523250
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3831425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4754.51293
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 85
Rwork0.245 1500

+
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