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- PDB-8jnp: Crystal structure of cytochrome P450 CftA from Streptomyces torul... -

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Basic information

Entry
Database: PDB / ID: 8jnp
TitleCrystal structure of cytochrome P450 CftA from Streptomyces torulosus NRRL B-3889, in complex with the substrate ikarugamycin
ComponentsCytochrome P450 CftA
KeywordsOXIDOREDUCTASE / Actinomadura viridis / hydrolase / Lobophorin / deglycosylation
Function / homologyChem-EIA / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStreptomyces torulosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJiang, P. / Zhang, L.P. / Zhang, C.S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177118 China
National Natural Science Foundation of China (NSFC)31630004 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates.
Authors: Jiang, P. / Jin, H. / Zhang, G. / Zhang, W. / Liu, W. / Zhu, Y. / Zhang, C. / Zhang, L.
History
DepositionJun 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 CftA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1843
Polymers44,0891
Non-polymers1,0952
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-26 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.197, 68.383, 108.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450 CftA


Mass: 44088.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces torulosus (bacteria) / Strain: NRRL B-3889 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-EIA / (1Z,3E,5S,7R,8R,10R,11R,12S,15R,16S,18Z,25S)-11-ethyl-2-hydroxy-10-methyl-21,26-diazapentacyclo[23.2.1.05,16.07,15.08,12]octacosa-1(2),3,13,18-tetraene-20,27,28-trione / ikarugamycin


Mass: 478.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H38N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M sodium chloride, 0.1M MES, 20% W/V PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→19.06 Å / Num. obs: 34584 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Χ2: 0.97 / Net I/σ(I): 13.5 / Num. measured all: 362272
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.559 / Num. measured all: 18120 / Num. unique obs: 2504 / CC1/2: 0.926 / Rpim(I) all: 0.222 / Rrim(I) all: 0.602 / Χ2: 0.48 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
AimlessCCP4Interface 7.1.015data scaling
CrysalisPro171.39.7edata reduction
MOLREPCCP4Interface 7.1.015phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.06 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 1678 4.91 %
Rwork0.1879 --
obs0.1903 34179 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 78 388 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113204
X-RAY DIFFRACTIONf_angle_d1.2434378
X-RAY DIFFRACTIONf_dihedral_angle_d8.512477
X-RAY DIFFRACTIONf_chiral_restr0.06486
X-RAY DIFFRACTIONf_plane_restr0.012577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.2811430.21472686X-RAY DIFFRACTION100
2.06-2.130.24641290.20582706X-RAY DIFFRACTION100
2.13-2.20.30951180.23692680X-RAY DIFFRACTION99
2.2-2.290.40941550.28362648X-RAY DIFFRACTION98
2.29-2.390.2491470.22332630X-RAY DIFFRACTION97
2.39-2.520.21051430.19952666X-RAY DIFFRACTION99
2.52-2.680.24081420.19912658X-RAY DIFFRACTION98
2.68-2.880.27051360.19182698X-RAY DIFFRACTION99
2.88-3.170.24191260.19452724X-RAY DIFFRACTION99
3.17-3.630.24661430.18572733X-RAY DIFFRACTION99
3.63-4.560.19411550.15382778X-RAY DIFFRACTION100
4.56-19.060.18911410.16062894X-RAY DIFFRACTION100

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