[English] 日本語
Yorodumi
- PDB-1n6b: Microsomal Cytochrome P450 2C5/3LVdH Complex with a dimethyl deri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n6b
TitleMicrosomal Cytochrome P450 2C5/3LVdH Complex with a dimethyl derivative of sulfaphenazole
ComponentsCytochrome P450 2C5
KeywordsOXIDOREDUCTASE / MEMBRANE PROTEIN / PROGESTERONE 21-HYDROXYLASE / BENZO(A) / PYRENE HYDROXYLASE / ESTRADIOL 2-HYDROXYLASE / P450 / CYP2C5 / DIMETHYLSULFAPHENAZOLE COMPLEX
Function / homology
Function and homology information


organic acid metabolic process / unspecific monooxygenase / aromatase activity / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
: / Cytochrome P450, E-class, group I / 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-DMZ / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2C5
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWester, M.R. / Johnson, E.F. / Marques-Soares, C. / Dansette, P.M. / Mansuy, D. / Stout, C.D.
Citation
Journal: Biochemistry / Year: 2003
Title: Structure of a Substrate Complex of Mammalian Cytochrome P450 2C5 at 2.3 A Resolution: Evidence for Multiple Substrate Binding Modes
Authors: Wester, M.R. / Johnson, E.F. / Marques-Soares, C. / Dansette, P.M. / Mansuy, D. / Stout, C.D.
#1: Journal: Mol.Cell / Year: 2000
Title: Mammalian Microsomal Cytochrome P450 Monooxygenase: Structural Adaptations for Membrane Binding and Functional Diversity
Authors: Williams, P.A. / Cosme, J. / Sridhar, V. / Johnson, E.F. / McRee, D.E.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Engineering Microsomal Cytochrome P450 2C5 to be a Soluble, Monomeric Enzyme. Mutations that Alter Aggregation, Phospholipid Dependence of Catalysis, and Membrane Binding
Authors: Cosme, J. / Johnson, E.F.
History
DepositionNov 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 2C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0205
Polymers53,8841
Non-polymers1,1364
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Cytochrome P450 2C5
hetero molecules

A: Cytochrome P450 2C5
hetero molecules

A: Cytochrome P450 2C5
hetero molecules

A: Cytochrome P450 2C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,08120
Polymers215,5374
Non-polymers4,54416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area15900 Å2
ΔGint-242 kcal/mol
Surface area75480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.330, 134.290, 171.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

-
Components

#1: Protein Cytochrome P450 2C5 / CYPIIC5 / P450 1 / Progesterone 21-hydroxylase / P450IIC5


Mass: 53884.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2C5 / Organ: LIVER / Plasmid: PCW / Production host: Escherichia coli (E. coli) / References: UniProt: P00179, unspecific monooxygenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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-DMZ / 4-METHYL-N-METHYL-N-(2-PHENYL-2H-PYRAZOL-3-YL)BENZENESULFONAMIDE / DIMETHYLSULFAPHENAZOLE


Mass: 327.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: AMMONIUM SULFATE, CYMAL5, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.24 mMP4501drop
20.24 mMDMZ1drop
32.4 mMCYMAL-5 detergent1drop
41.1 Mammonium sulfate1drop
50.05 MHEPES1droppH7.5
60.5 %PEG4001drop
720 mMpotassium phosphate1droppH7.4
8200 mM1dropNaCl
90.4 mMEDTA1drop
100.08 mMdithiothreitol1drop
118 %glycerol1drop
122.2 Mammonium sulfate1reservoir
130.1 MHEPES1reservoirpH7.5
141 %PEG4001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37253 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.479 / % possible all: 78.5
Reflection
*PLUS
Num. measured all: 153575
Reflection shell
*PLUS
% possible obs: 78.5 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT6

1dt6


Resolution: 2.3→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1698 -RANDOM
Rwork0.257 ---
obs0.257 37253 96.6 %-
all-37253 --
Displacement parametersBiso mean: 60.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 0 76 118 3891
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.29
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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