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- PDB-1pkf: Crystal Structure of Epothilone D-bound Cytochrome P450epoK -

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Basic information

Entry
Database: PDB / ID: 1pkf
TitleCrystal Structure of Epothilone D-bound Cytochrome P450epoK
Componentscytochrome p450EpoK
KeywordsOXIDOREDUCTASE / CYTOCHROME P450EPOK / HEME-ENZYME
Function / homology
Function and homology information


epothilone biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EPOTHILONE D / PROTOPORPHYRIN IX CONTAINING FE / Epothilone C/D epoxidase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsNagano, S. / Li, H. / Shimizu, H. / Nishida, C. / Ogura, H. / Ortiz de Montellano, P.R. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structures of Epothilone D-bound, Epothilone B-bound, and Substrate-free Forms of Cytochrome P450epoK
Authors: Nagano, S. / Li, H. / Shimizu, H. / Nishida, C. / Ogura, H. / Ortiz de Montellano, P.R. / Poulos, T.L.
History
DepositionJun 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytochrome p450EpoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9323
Polymers46,8231
Non-polymers1,1082
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.430, 60.430, 252.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein cytochrome p450EpoK


Mass: 46823.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KIZ4
#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-EPD / EPOTHILONE D


Mass: 491.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H41NO5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: PEG 550, Glycine, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 23K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 %PEG550 MME1reservoir
20.05 Mglycine1reservoirpH8.4

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2002
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25935 / % possible obs: 96.2 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 33.9
Reflection shellResolution: 2.1→2.154 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1348 / % possible all: 96.2
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / Num. obs: 27331 / Num. measured all: 167058
Reflection shell
*PLUS
% possible obs: 95.4 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.421 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1329 4.9 %RANDOM
Rwork0.219 ---
all0.22 25935 --
obs0.22 25935 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.099 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--1.24 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 77 200 3452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213326
X-RAY DIFFRACTIONr_bond_other_d0.0050.023136
X-RAY DIFFRACTIONr_angle_refined_deg1.442.0244524
X-RAY DIFFRACTIONr_angle_other_deg0.81937226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023677
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02709
X-RAY DIFFRACTIONr_nbd_refined0.2340.3802
X-RAY DIFFRACTIONr_nbd_other0.2730.33656
X-RAY DIFFRACTIONr_nbtor_other0.0920.51918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.5285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3380.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3970.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.43822013
X-RAY DIFFRACTIONr_mcangle_it2.53833245
X-RAY DIFFRACTIONr_scbond_it1.61121313
X-RAY DIFFRACTIONr_scangle_it2.38231279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 82
Rwork0.3 1890
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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