[English] 日本語
Yorodumi
- PDB-3r1b: Open crystal structure of cytochrome P450 2B4 covalently bound to... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r1b
TitleOpen crystal structure of cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / cytochrome P450 2B4 / monooxygenase / membrane protein / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
sucrose / PROTOPORPHYRIN IX CONTAINING FE / (4-tert-butylphenyl)acetaldehyde / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsGay, S.C. / Zhang, H. / Stout, C.D. / Hollenberg, P.F. / Halpert, J.R.
Citation
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: Gay, S.C. / Zhang, H. / Wilderman, P.R. / Roberts, A.G. / Liu, T. / Li, S. / Lin, H.L. / Zhang, Q. / Woods, V.L. / Stout, C.D. / Hollenberg, P.F. / Halpert, J.R.
#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.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 2B4
B: Cytochrome P450 2B4
C: Cytochrome P450 2B4
D: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,68921
Polymers216,6764
Non-polymers7,01317
Water00
1
A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2936
Polymers54,1691
Non-polymers2,1245
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2936
Polymers54,1691
Non-polymers2,1245
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3044
Polymers54,1691
Non-polymers1,1353
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7995
Polymers54,1691
Non-polymers1,6304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Cytochrome P450 2B4
D: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,09211
Polymers108,3382
Non-polymers3,7549
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-85 kcal/mol
Surface area42590 Å2
MethodPISA
6
B: Cytochrome P450 2B4
C: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,59710
Polymers108,3382
Non-polymers3,2598
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-82 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.924, 153.691, 129.665
Angle α, β, γ (deg.)90.00, 122.22, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#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.: 4
Mutation: E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, 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
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-TB2 / (4-tert-butylphenyl)acetaldehyde


Mass: 176.255 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H16O
#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.: 5 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
Nonpolymer detailsTHE PROTEIN WAS INCUBATED WITH TERT-BUTYLPHENYLACETYLENE, CATALASE, CYTOCHROME P450 REDUCTASE, AND ...THE PROTEIN WAS INCUBATED WITH TERT-BUTYLPHENYLACETYLENE, CATALASE, CYTOCHROME P450 REDUCTASE, AND CYTOCHROME B5. A SINGLE CATALYTIC P450 2B4 TURNOVER RESULTS IN A KETENE INTERMEDIATE, WHICH CONJUGATES TO THR 302. THIS CONJUGATED PROTEIN IS PUT DOWN FOR CRYSTALLIZATION. lIGAND CM5 A 605 IS MISSING 10 ATOMS SINCE THEY WERE NOT OBSERVED IN THE ELECTRON DENSITY MAPS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 12% (w/v) PEG 3350, pH 7.5, vapor diffusion, sitting drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 22, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→112.161 Å / Num. all: 63932 / Num. obs: 63932 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 84.22 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
3-3.163.10.5861.30.58699.9
3.16-3.353.20.3212.40.32199.8
3.35-3.593.20.2273.40.22799.7
3.59-3.873.20.145.20.1499.6
3.87-4.243.20.1046.40.10499.5
4.24-4.743.20.0887.30.08899.3
4.74-5.483.20.0798.10.07999.2
5.48-6.713.20.0758.40.07598.7
6.71-9.493.20.0648.60.06498.4
9.49-53.4323.10.0638.70.06397.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.63 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å53.43 Å
Translation3 Å53.43 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
SSRLBlue-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SUO

1suo


Resolution: 3→53.43 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.44 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.288 3092 5.07 %
Rwork0.242 --
obs0.244 61019 94.8 %
all-64352 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.04 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 100.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.4092 Å2-0 Å23.4714 Å2
2---9.6467 Å2-0 Å2
3---14.0559 Å2
Refinement stepCycle: LAST / Resolution: 3→53.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14023 0 476 0 14499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814884
X-RAY DIFFRACTIONf_angle_d1.35120347
X-RAY DIFFRACTIONf_dihedral_angle_d16.4135345
X-RAY DIFFRACTIONf_chiral_restr0.0782303
X-RAY DIFFRACTIONf_plane_restr0.012623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04690.42791460.35592344X-RAY DIFFRACTION85
3.0469-3.09680.3461290.3222385X-RAY DIFFRACTION86
3.0968-3.15020.3591190.3162426X-RAY DIFFRACTION88
3.1502-3.20750.40391310.29912504X-RAY DIFFRACTION91
3.2075-3.26920.34741260.29422588X-RAY DIFFRACTION93
3.2692-3.33590.33481560.28932595X-RAY DIFFRACTION93
3.3359-3.40840.29831330.27742556X-RAY DIFFRACTION93
3.4084-3.48770.32721490.2682528X-RAY DIFFRACTION93
3.4877-3.57490.30381120.26292518X-RAY DIFFRACTION91
3.5749-3.67150.29931490.27952708X-RAY DIFFRACTION97
3.6715-3.77960.32391440.25392731X-RAY DIFFRACTION99
3.7796-3.90150.25491500.23652705X-RAY DIFFRACTION97
3.9015-4.04090.27931420.23352659X-RAY DIFFRACTION96
4.0409-4.20260.28311380.23062682X-RAY DIFFRACTION98
4.2026-4.39380.27911450.22092751X-RAY DIFFRACTION98
4.3938-4.62540.30921560.21192719X-RAY DIFFRACTION98
4.6254-4.9150.2771510.21382744X-RAY DIFFRACTION99
4.915-5.29410.24461490.22552733X-RAY DIFFRACTION99
5.2941-5.82630.34611380.26192751X-RAY DIFFRACTION99
5.8263-6.6680.26991340.27042758X-RAY DIFFRACTION98
6.668-8.39580.26541510.22412760X-RAY DIFFRACTION98
8.3958-53.44060.23661440.20992782X-RAY DIFFRACTION97

+
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