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- PDB-1dt6: STRUCTURE OF MAMMALIAN CYTOCHROME P450 2C5 -

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Basic information

Entry
Database: PDB / ID: 1dt6
TitleSTRUCTURE OF MAMMALIAN CYTOCHROME P450 2C5
ComponentsCYTOCHROME P450 2C5
KeywordsOXIDOREDUCTASE / membrane protein / progesterone 21-hydroxylase / benzo(a)pyrene hydroxylase / estradiol 2-hydroxylase / P450 / CYP2C5
Function / homology
Function and homology information


organic acid metabolic process / unspecific monooxygenase / aromatase activity / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
: / 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 / SAMARIUM (III) ION / Cytochrome P450 2C5
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsWilliams, P.A. / Cosme, J. / Sridhar, V. / Johnson, E.F. / McRee, D.E.
Citation
Journal: Mol.Cell / Year: 2000
Title: Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity.
Authors: Williams, P.A. / Cosme, J. / Sridhar, V. / Johnson, E.F. / McRee, D.E.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Engineering Microsomal Cytochrome P450 2C5 to be a Soluble, Monomeric Enzyme. Mutations that Alter Aggregation, Phospholipid Dependence of Catalysis and Membrane Binding
Authors: Cosme, J. / Johnson, E.F.
History
DepositionJan 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 3, 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450 2C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9396
Polymers53,8841
Non-polymers1,0555
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CYTOCHROME P450 2C5
hetero molecules

A: CYTOCHROME P450 2C5
hetero molecules

A: CYTOCHROME P450 2C5
hetero molecules

A: CYTOCHROME P450 2C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,75724
Polymers215,5374
Non-polymers4,22020
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12040 Å2
ΔGint-280 kcal/mol
Surface area78710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.700, 132.000, 172.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-502-

SM

DetailsThe biological assembly is the monomer found in the asymmetric unit.

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Components

#1: Protein CYTOCHROME P450 2C5 / PROGESTERONE 21-HYDROXYLASE / CYPIIC5 P450 1 / P450IIC5


Mass: 53884.250 Da / Num. of mol.: 1
Fragment: CYP2C5 WITH MEMBRANE SPANNING RESIDUES 3-21 DELETED AND A 4 RESIDUE HISTIDINE TAG AT THE C-TERMINUS CONTAINING ADDITIONAL INTERNAL MUTATIONS
Mutation: D2A, H24S, G25S, N202H, R206E, I207L, S209G, S210T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: LIVER / Plasmid: PCW / Production host: Escherichia coli (E. coli) / References: UniProt: P00179, unspecific monooxygenase
#2: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sm
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.5 M ammonium sulphate, 0.1 M sodium cacodylate, 2.4mM CYMAL-5, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 24K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
22.5 Mammonium sulfate1reservoir
30.1 Msodium cacodylate1reservoir
42.4 mMCYMAL-51reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM1411.739
SYNCHROTRONESRF BM1420.849
SYNCHROTRONSSRL BL7-131.08
SYNCHROTRONSSRL BL9-140.97
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEApr 1, 1998
MARRESEARCH2IMAGE PLATEApr 1, 1998
MARRESEARCH3IMAGE PLATEMar 6, 1998
MARRESEARCH4IMAGE PLATEMay 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7391
20.8491
31.081
40.971
ReflectionResolution: 3→25 Å / Num. all: 16332 / Num. obs: 63981 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 4.7
Reflection shellResolution: 3→3.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.318 / % possible all: 75.6
Reflection
*PLUS
Num. obs: 16332 / Num. measured all: 63981
Reflection shell
*PLUS
% possible obs: 75.6 %

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Processing

Software
NameVersionClassification
CNSrefinement
SCALAdata scaling
XTALVIEWrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 3→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 809 -random 5%
Rwork0.238 ---
all0.241 16288 --
obs0.241 16288 93.2 %-
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 59 0 3648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.009
X-RAY DIFFRACTIONc_angle_deg1.77
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d

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