[English] 日本語
Yorodumi
- PDB-3uas: Cytochrome P450 2B4 covalently bound to the mechanism-based inact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uas
TitleCytochrome P450 2B4 covalently bound to the mechanism-based inactivator 9-ethynylphenanthrene
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / P450 / cytochrome P450 2B4 / monooxygenase / membrane protein / CYP 2B4 / CYP LM2
Function / homology
Function and homology information


arachidonic acid epoxygenase activity / epoxygenase P450 pathway / unspecific monooxygenase / aromatase activity / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2B-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
phenanthren-9-ylacetaldehyde / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.939 Å
AuthorsGay, S.C. / Zhang, H. / Shah, M.B. / Stout, C.D. / Halpert, J.R. / Hollenberg, P.F.
Citation
Journal: Biochemistry / Year: 2013
Title: Potent Mechanism-Based Inactivation of Cytochrome P450 2B4 by 9-Ethynylphenanthrene: Implications for Allosteric Modulation of Cytochrome P450 Catalysis.
Authors: Zhang, H. / Gay, S.C. / Shah, M. / Foroozesh, M. / Liu, J. / Osawa, Y. / Zhang, Q. / Stout, C.D. / Halpert, J.R. / Hollenberg, P.F.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.
Authors: Zhao, Y. / White, M.A. / Muralidhara, B.K. / Sun, L. / Halpert, J.R. / Stout, C.D.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding.
Authors: Scott, E.E. / White, M.A. / He, Y.A. / Johnson, E.F. / Stout, C.D. / Halpert, J.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution.
Authors: Scott, E.E. / He, Y.A. / Wester, M.R. / White, M.A. / Chin, C.C. / Halpert, J.R. / Johnson, E.F. / Stout, C.D.
#4: Journal: Biochemistry / Year: 2007
Title: Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
Authors: Zhao, Y. / Sun, L. / Muralidhara, B.K. / Kumar, S. / White, M.A. / Stout, C.D. / Halpert, J.R.
#5: Journal: Biochemistry / Year: 2009
Title: Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand-induced structural response through alpha-helical repositioning.
Authors: Gay, S.C. / Sun, L. / Maekawa, K. / Halpert, J.R. / Stout, C.D.
#6: Journal: Biochemistry / Year: 2010
Title: Structures of cytochrome P450 2B4 complexed with the antiplatelet drugs ticlopidine and clopidogrel .
Authors: Gay, S.C. / Roberts, A.G. / Maekawa, K. / Talakad, J.C. / Hong, W.X. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
#7: Journal: J.Biol.Chem. / Year: 2010
Title: Plasticity of cytochrome P450 2B4 as investigated by hydrogen-deuterium exchange mass spectrometry and X-ray crystallography.
Authors: Wilderman, P.R. / Shah, M.B. / Liu, T. / Li, S. / Hsu, S. / Roberts, A.G. / Goodlett, D.R. / Zhang, Q. / Woods, V.L. / Stout, C.D. / Halpert, J.R.
#8: Journal: Biochemistry / Year: 2011
Title: Structural Analysis of Mammalian Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator tert-Butylphenylacetylene: Insight into Partial Enzymatic Activity
Authors: C Gay, S. / Zhang, H. / Wilderman, P.R. / Roberts, A.G. / Liu, T. / Li, S. / Lin, H.L. / Woods Jr., V.L. / Stout, C.D. / Hollenberg, P.F. / Halpert, J.R.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.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 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8276
Polymers54,1691
Non-polymers1,6585
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.155, 90.155, 148.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological unit is a monomer. There is one biological unit in the asymmetric unit (chain A).

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 2B4 / CYPIIB4 / Cytochrome P450 isozyme 2 / Cytochrome P450 LM2 / Cytochrome P450 type B0 / Cytochrome P450 type B1


Mass: 54169.082 Da / Num. of mol.: 1 / Mutation: H226Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2B4 / Plasmid: PKK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P00178, unspecific monooxygenase

-
Non-polymers , 5 types, 77 molecules

#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-0BV / phenanthren-9-ylacetaldehyde / 9-ethylphenanthrene, oxidized and bound form


Mass: 220.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsP221S MUTATION IS DUE TO AN ERROR IN THE O00178 SEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris, 20% (w/v) PEG 3000, 0.2 M calcium acetate, pH 7.0, vapor diffusion, sitting drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 5, 2011
RadiationMonochromator: QUAZAR MX MICROFOCUS SOURCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.939→78.08 Å / Num. all: 15475 / Num. obs: 15444 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 12.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allNum. unique obs% possible all
2.939-2.963.610.3952.1417417492.6
2.96-3.025.990.353.17876876100
3.02-3.086.270.3033.85781781100
3.08-3.156.280.2794.39886886100
3.15-3.226.460.2495.15787787100
3.22-3.36.570.225.93818818100
3.3-3.396.720.2016.93853853100
3.39-3.496.920.1958.1842842100
3.49-3.670.2129.28821821100
3.6-3.727.120.21210.4378978999.9
3.72-3.867.390.16612.6804804100
3.86-4.027.770.12713.5677477499.9
4.02-4.217.980.11715.33780780100
4.21-4.448.270.11918.2378678699.9
4.44-4.738.640.09620.38786786100
4.73-5.118.860.08321.3778578599.9
5.11-5.658.810.08618.6777777799.9
5.65-6.58.780.09416.8777777799.9
6.5-8.288.620.07222.66774774100
8.28-53.837.550.04630.9177477498.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.94 Å53.83 Å
Translation2.94 Å53.83 Å

-
Processing

Software
NameVersionClassificationNB
SAINTdata scaling
XPREP2008/2 for Windowsdata reduction
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SUO

1suo


Resolution: 2.939→78.08 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.804 / WRfactor Rfree: 0.2634 / WRfactor Rwork: 0.2146 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7869 / SU B: 19.568 / SU ML: 0.363 / SU Rfree: 0.4576 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2961 765 5 %RANDOM
Rwork0.2429 ---
all0.2455 15435 --
obs0.2455 15379 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.73 Å2 / Biso mean: 28.641 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å20 Å2
2---0.9 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.939→78.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 116 72 3884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223905
X-RAY DIFFRACTIONr_angle_refined_deg0.9522.0235300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7745457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46722.64178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5515637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6641534
X-RAY DIFFRACTIONr_chiral_restr0.0650.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212972
X-RAY DIFFRACTIONr_mcbond_it0.2691.52307
X-RAY DIFFRACTIONr_mcangle_it0.50123745
X-RAY DIFFRACTIONr_scbond_it0.48631598
X-RAY DIFFRACTIONr_scangle_it0.8934.51555
LS refinement shellResolution: 2.939→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 71 -
Rwork0.299 1045 -
all-1116 -
obs--98.85 %

+
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://pdbjlvh1.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