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- PDB-3g93: Single ligand occupancy crystal structure of cytochrome P450 2B4 ... -

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Basic information

Entry
Database: PDB / ID: 3g93
TitleSingle 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


arachidonate 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 ...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: 3.2 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 12, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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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)220,07912
Polymers216,6764
Non-polymers3,4038
Water61334
1
C: Cytochrome P450 2B4
hetero molecules

D: Cytochrome P450 2B4
hetero molecules

A: Cytochrome P450 2B4
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,07912
Polymers216,6764
Non-polymers3,4038
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+3/2,-y,z+1/21
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area23170 Å2
ΔGint-251 kcal/mol
Surface area69440 Å2
MethodPISA
2
A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2544
Polymers54,1691
Non-polymers1,0853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7862
Polymers54,1691
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0203
Polymers54,1691
Non-polymers8512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0203
Polymers54,1691
Non-polymers8512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.910, 151.815, 181.583
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 27:134 or resseq 139:229 or resseq...
21chain B and (resseq 28:132 or resseq 140:274 or resseq 285:470 or resseq 479:492 )
31chain C and (resseq 28:132 or resseq 140:229 or resseq...
41chain D and (resseq 28:132 or resseq 141:229 or resseq...

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
11LYSLYSASPASPAA27 - 1348 - 115
12LYSLYSGLYGLYAA139 - 229120 - 210
13ARGARGLYSLYSAA236 - 274217 - 255
14HISHISGLUGLUAA284 - 474265 - 455
15ASNASNHISHISAA479 - 492460 - 473
21GLYGLYMETMETBB28 - 1329 - 113
22ARGARGLYSLYSBB140 - 274121 - 255
23HISHISLEULEUBB285 - 470266 - 451
24ASNASNHISHISBB479 - 492460 - 473
31GLYGLYMETMETCC28 - 1329 - 113
32ARGARGGLYGLYCC140 - 229121 - 210
33ARGARGGLUGLUCC236 - 273217 - 254
34PHEPHEPROPROCC283 - 472264 - 453
35VALVALARGARGCC480 - 491461 - 472
41GLYGLYMETMETDD28 - 1329 - 113
42SERSERGLYGLYDD141 - 229122 - 210
43ASNASNASPASPDD237 - 275218 - 256
44HISHISPROPRODD285 - 472266 - 453
45VALVALARGARGDD480 - 491461 - 472

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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.: 4 / Source method: obtained synthetically / Formula: C16H14N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 8% 2-methyl-2,4-pentadediol, 13% PEG 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2008
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→48.747 Å / Num. obs: 73790 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 50.19 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 4.432
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2903 / Rsym value: 0.506 / % possible all: 99.5

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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: A chain from PDB ID 3G5N

3g5n


Resolution: 3.2→48.747 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.49 / σ(F): 0.03 / Phase error: 26.19 / Stereochemistry target values: ML
Details: Friedel pairs were used for phasing and refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3452 5.01 %random
Rwork0.237 65455 --
obs0.239 68907 90.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.916 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 137.03 Å2 / Biso mean: 44.89 Å2 / Biso min: 3.25 Å2
Baniso -1Baniso -2Baniso -3
1-16.201 Å2-0 Å2-0 Å2
2---6.201 Å20 Å2
3----9.999 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13435 0 244 34 13713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01514052
X-RAY DIFFRACTIONf_angle_d1.46719225
X-RAY DIFFRACTIONf_chiral_restr0.0842180
X-RAY DIFFRACTIONf_plane_restr0.0092489
X-RAY DIFFRACTIONf_dihedral_angle_d19.2964802
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3239X-RAY DIFFRACTIONPOSITIONAL
12B3239X-RAY DIFFRACTIONPOSITIONAL0.37
13C3259X-RAY DIFFRACTIONPOSITIONAL0.332
14D3207X-RAY DIFFRACTIONPOSITIONAL0.222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.2440.3291070.312368247581
3.244-3.290.3311360.2922426256284
3.29-3.3390.3271370.2872451258884
3.339-3.3910.3341390.2992436257585
3.391-3.4470.3811190.3522423254282
3.447-3.5070.3541430.2972373251683
3.507-3.570.2891460.2482559270589
3.57-3.6390.3061410.2632573271488
3.639-3.7130.3381460.2952485263186
3.713-3.7940.2931510.2552633278491
3.794-3.8820.3181450.262552269789
3.882-3.9790.381260.2882555268187
3.979-4.0870.2741210.2282755287694
4.087-4.2070.2611630.2072688285193
4.207-4.3430.211190.1972795291494
4.343-4.4980.2141220.1862753287595
4.498-4.6770.181480.172717286594
4.677-4.890.1811300.1782756288694
4.89-5.1480.2161520.1932724287693
5.148-5.470.2451240.212739286394
5.47-5.8920.2511570.2212674283193
5.892-6.4830.2731260.2192745287194
6.483-7.4190.21430.2092751289494
7.419-9.3360.2071820.1732746292896
9.336-48.7530.1971290.1892778290795

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