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- PDB-3g5n: Triple ligand occupancy crystal structure of cytochrome P450 2B4 ... -

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Basic information

Entry
Database: PDB / ID: 3g5n
TitleTriple ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / P450 / cytochrome P450 2B4 / monooxygenase / membrane protein / CYP 2B4 / CYP LM2 / Endoplasmic reticulum / Heme / Iron / Membrane / Metal-binding / Microsome / Phosphoprotein / Polymorphism
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
PROTOPORPHYRIN IX CONTAINING FE / 1-(biphenyl-4-ylmethyl)-1H-imidazole / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGay, S.C. / Sun, L. / Maekawa, K. / Halpert, J.R. / Stout, C.D.
Citation
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.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 {angstrom} resolution: Insight into the range of P450 conformations and 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: 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.
#4: 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.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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.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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)223,93224
Polymers216,6764
Non-polymers7,25620
Water3,243180
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29120 Å2
ΔGint-238 kcal/mol
Surface area66330 Å2
MethodPISA
2
A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7495
Polymers54,1691
Non-polymers1,5804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2177
Polymers54,1691
Non-polymers2,0486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9836
Polymers54,1691
Non-polymers1,8145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9836
Polymers54,1691
Non-polymers1,8145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.696, 152.526, 181.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 28:130 or resseq 140:256 or resseq 261:273 or resseq 285:492 )
21chain B and (resseq 28:130 or resseq 140:256 or resseq 261:272 or resseq 285:492 )
31chain C and (resseq 28:130 or resseq 140:256 or resseq 261:273 or resseq 285:492 )
41chain D and (resseq 28:130 or resseq 140:256 or resseq 261:273 or resseq 285:492 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALAAA28 - 1309 - 111
12ARGARGLEULEUAA140 - 256121 - 237
13PROPROGLUGLUAA261 - 273242 - 254
14HISHISHISHISAA285 - 492266 - 473
21GLYGLYALAALABB28 - 1309 - 111
22ARGARGLEULEUBB140 - 256121 - 237
23PROPROMETMETBB261 - 272242 - 253
24HISHISHISHISBB285 - 492266 - 473
31GLYGLYALAALACC28 - 1309 - 111
32ARGARGLEULEUCC140 - 256121 - 237
33PROPROGLUGLUCC261 - 273242 - 254
34HISHISHISHISCC285 - 492266 - 473
41GLYGLYALAALADD28 - 1309 - 111
42ARGARGLEULEUDD140 - 256121 - 237
43PROPROGLUGLUDD261 - 273242 - 254
44HISHISHISHISDD285 - 492266 - 473

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Components

#1: Protein
Cytochrome P450 2B4 / CYPIIB4 / P450-LM2 / Isozyme 2 / P450 types B0 and B1


Mass: 54169.082 Da / Num. of mol.: 4
Mutation: E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, P221S, H226Y
Source method: isolated from a genetically manipulated source
Details: Deleted residues 3-21, E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, 4x Cterm His tag
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: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PB2 / 1-(biphenyl-4-ylmethyl)-1H-imidazole


Mass: 234.296 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H14N2
#4: 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.: 4 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS INDICATE THAT THERE IS AN ERROR IN THE SEQUENCE DATABASE REFERENCE AT RESIDUE 221

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M HEPES, 10% 2-methyl-2,4-pentanediol, 10% PEG 6000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2007
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→48.457 Å / Num. obs: 81702 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 56.03 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 5.641
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.1 / Num. unique all: 5714 / Rsym value: 0.656 / % possible all: 93.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble of PDB entries 1PO5, 2BDM, 1SUO, 2Q6N

1po5

2bdm

1suo

2q6n


Resolution: 2.5→45.476 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 4088 5.01 %random
Rwork0.2184 ---
obs0.2199 81584 97.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.243 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 143.71 Å2 / Biso mean: 62.828 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.7066 Å2-0 Å2-0 Å2
2---1.9532 Å20 Å2
3----1.7534 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14102 0 452 180 14734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214966
X-RAY DIFFRACTIONf_angle_d1.83820388
X-RAY DIFFRACTIONf_chiral_restr0.1252247
X-RAY DIFFRACTIONf_plane_restr0.0092626
X-RAY DIFFRACTIONf_dihedral_angle_d20.4465280
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3404X-RAY DIFFRACTIONPOSITIONAL
12B3404X-RAY DIFFRACTIONPOSITIONAL0.359
13C3382X-RAY DIFFRACTIONPOSITIONAL0.376
14D3409X-RAY DIFFRACTIONPOSITIONAL0.431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.530.41360.3382523265993
2.53-2.560.3171520.3052505265792
2.56-2.5930.3131150.2772551266694
2.593-2.6270.3191390.2932556269593
2.627-2.6630.3231320.2972491262393
2.663-2.7010.3731410.3142517265892
2.701-2.7410.2941460.2642519266593
2.741-2.7840.2981360.252584272094
2.784-2.830.2741180.2582596271495
2.83-2.8780.3091160.2512646276296
2.878-2.9310.2871180.2592631274996
2.931-2.9870.3061250.262657278297
2.987-3.0480.2781420.2612670281298
3.048-3.1140.2891500.2572692284298
3.114-3.1870.3331390.2482702284199
3.187-3.2660.2791440.242700284499
3.266-3.3550.2791490.24227342883100
3.355-3.4530.2941550.2422731288699
3.453-3.5650.2971470.22727282875100
3.565-3.6920.2381560.2227132869100
3.692-3.840.2241380.20927632901100
3.84-4.0150.2411570.20427462903100
4.015-4.2260.2271500.18227372887100
4.226-4.4910.1841610.16827722933100
4.491-4.8370.171380.15727862924100
4.837-5.3230.1981440.1732764290899
5.323-6.0920.2151440.1912796294099
6.092-7.6690.2341540.1962774292898
7.669-45.4830.181460.1722912305897

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