[English] 日本語
Yorodumi
- PDB-3gph: Human cytochrome P450 2E1 in complex with omega-imidazolyl-decano... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gph
TitleHuman cytochrome P450 2E1 in complex with omega-imidazolyl-decanoic acid
ComponentsCytochrome P450 2E1
KeywordsOXIDOREDUCTASE / CYP2E1 / P450 2E1 / monooxygenase / acetaminophen / heme / fatty acid hydroxylase / Metal-binding
Function / homology
Function and homology information


: / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity ...: / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / lipid hydroxylation / 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 / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / Xenobiotics / Paracetamol ADME / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / long-chain fatty acid biosynthetic process / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / Hsp70 protein binding / xenobiotic metabolic process / monooxygenase activity / response to bacterium / Hsp90 protein binding / oxygen binding / mitochondrial inner membrane / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2E-like / : / 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 ...Cytochrome P450, E-class, group I, CYP2E-like / : / 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
PROTOPORPHYRIN IX CONTAINING FE / 10-(1H-imidazol-1-yl)decanoic acid / Cytochrome P450 2E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPorubsky, P.R. / Battaile, K.P. / Scott, E.E.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode.
Authors: Porubsky, P.R. / Battaile, K.P. / Scott, E.E.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
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 / 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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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 2E1
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8276
Polymers110,1172
Non-polymers1,7104
Water45025
1
A: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9133
Polymers55,0581
Non-polymers8552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9133
Polymers55,0581
Non-polymers8552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.709, 70.709, 222.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Cytochrome P450 2E1 / CYPIIE1 / P450-J


Mass: 55058.488 Da / Num. of mol.: 2 / Fragment: UNP residues 32-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2E, CYP2E1 / Plasmid: pKK2E1dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P05181, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OID / 10-(1H-imidazol-1-yl)decanoic acid / 10-imidazolyl-decanoic acid


Mass: 238.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na HEPES, 5% Isopropanol, 20% PEG 2000 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 2, 2008
Details: Sagitally focused second crystal, vertical focusing via a one-meter, Pt/Pd-coated cylindrically focusing mirror
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 28495 / Num. obs: 28493 / % possible obs: 95.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 51.075 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.071
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.457 / Num. unique all: 2034 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E61

3e61


Resolution: 2.7→31.31 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.86 / SU B: 14.75 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.42
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28261 1442 5.1 %RANDOM
Rwork0.21245 ---
obs0.21609 27040 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.748 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7530 0 120 25 7675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227881
X-RAY DIFFRACTIONr_angle_refined_deg1.9092.01110694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5175920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53723.164373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.783151345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0481558
X-RAY DIFFRACTIONr_chiral_restr0.1360.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026044
X-RAY DIFFRACTIONr_nbd_refined0.2360.23654
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.246
X-RAY DIFFRACTIONr_mcbond_it0.6771.54812
X-RAY DIFFRACTIONr_mcangle_it1.17227538
X-RAY DIFFRACTIONr_scbond_it1.82833501
X-RAY DIFFRACTIONr_scangle_it2.7974.53151
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 97 -
Rwork0.266 1937 -
obs--93.47 %

+
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