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- PDB-8fz8: Structure of cytochrome P450sky2 -

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Basic information

Entry
Database: PDB / ID: 8fz8
TitleStructure of cytochrome P450sky2
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450sky2 / epoxidation
Function / homology
Function and homology information


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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OCTANOIC ACID (CAPRYLIC ACID) / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces nodosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMurarka, V.C. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131920 United States
CitationJournal: Org.Biomol.Chem. / Year: 2024
Title: Biosynthesis of a new skyllamycin in Streptomyces nodosus : a cytochrome P450 forms an epoxide in the cinnamoyl chain.
Authors: Song, Y. / Amaya, J.A. / Murarka, V.C. / Mendez, H. / Hogan, M. / Muldoon, J. / Evans, P. / Ortin, Y. / Kelly, S.L. / Lamb, D.C. / Poulos, T.L. / Caffrey, P.
History
DepositionJan 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9453
Polymers45,1851
Non-polymers7612
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.980, 97.850, 52.500
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 /


Mass: 45184.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nodosus (bacteria) / Gene: CP978_29155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5P2W9N6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M Tris:HCl buffer pH 8.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.43→52.29 Å / Num. obs: 64363 / % possible obs: 96.6 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.03 / Rrim(I) all: 0.063 / Χ2: 0.99 / Net I/σ(I): 11.9 / Num. measured all: 253881
Reflection shellResolution: 1.43→1.45 Å / % possible obs: 97.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.418 / Num. measured all: 12781 / Num. unique obs: 3208 / CC1/2: 0.871 / Rpim(I) all: 0.238 / Rrim(I) all: 0.483 / Χ2: 0.64 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→35.84 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1826 2000 3.11 %
Rwork0.1633 --
obs0.164 64284 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 53 406 3530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063362
X-RAY DIFFRACTIONf_angle_d0.8954617
X-RAY DIFFRACTIONf_dihedral_angle_d18.4171318
X-RAY DIFFRACTIONf_chiral_restr0.074519
X-RAY DIFFRACTIONf_plane_restr0.007608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.470.26481440.21964459X-RAY DIFFRACTION97
1.47-1.510.24761420.2034478X-RAY DIFFRACTION97
1.51-1.550.19881420.19354402X-RAY DIFFRACTION96
1.55-1.60.21041390.1884319X-RAY DIFFRACTION94
1.6-1.660.20661450.17614520X-RAY DIFFRACTION98
1.66-1.720.24091430.18054470X-RAY DIFFRACTION98
1.72-1.80.21881430.17914453X-RAY DIFFRACTION96
1.8-1.90.19371390.17784336X-RAY DIFFRACTION94
1.9-2.020.19041460.16364503X-RAY DIFFRACTION98
2.02-2.170.18361430.16264470X-RAY DIFFRACTION97
2.17-2.390.18711410.15594395X-RAY DIFFRACTION95
2.39-2.740.17171450.16654515X-RAY DIFFRACTION98
2.74-3.450.18051420.1574395X-RAY DIFFRACTION95
3.45-35.840.15081460.14594569X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 9.0878 Å / Origin y: 9.7804 Å / Origin z: 4.4395 Å
111213212223313233
T0.0848 Å20.0003 Å2-0.0177 Å2-0.1083 Å2-0.0046 Å2--0.1027 Å2
L0.4229 °2-0.0338 °2-0.0373 °2-1.0758 °20.0989 °2--0.5571 °2
S0.0068 Å °-0.0066 Å °0.0097 Å °-0.0447 Å °-0.0096 Å °-0.0477 Å °0.0071 Å °0.0483 Å °0.0026 Å °
Refinement TLS groupSelection details: all

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