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

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Basic information

Entry
Database: PDB / ID: 8jnq
TitleCrystal structure of cytochrome P450 CftA from Streptomyces torulosus NRRL B-3889, in complex with a substrate compound c
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Actinomadura viridis / hydrolase / Lobophorin / deglycosylation
Function / homologyChem-EIU / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2254
Polymers44,0891
Non-polymers1,1363
Water5,332296
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 area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.730, 68.436, 108.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cytochrome P450


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-EIU / (1Z,3E,5E,7S,8R,10S,11R,13R,15R,16E,18E,25S)-11-ethyl-2,7-dihydroxy-10-methyl-21,26-diazatetracyclo[23.2.1.09,13.08,15]octacosa-1(2),3,5,16,18-pentaene-20,27,28-trione


Mass: 496.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Lithium chloride, 0.1M MES pH 6.0, 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: Jun 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→19.47 Å / Num. obs: 33699 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 22.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.03 / Rrim(I) all: 0.089 / Χ2: 0.96 / Net I/σ(I): 16.6 / Num. measured all: 270689
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.812 / Num. measured all: 11546 / Num. unique obs: 2444 / CC1/2: 0.689 / Rpim(I) all: 0.417 / Rrim(I) all: 0.916 / Χ2: 0.94 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisPro171.39.7edata reduction
AimlessCCP4Interface 7.1.015data scaling
MOLREPCCP4Interface 7.1.015phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.47 Å / SU ML: 0.2347 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 1650 4.91 %
Rwork0.1879 31989 -
obs0.19 33639 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.64 Å2
Refinement stepCycle: LAST / Resolution: 2→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 80 296 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733198
X-RAY DIFFRACTIONf_angle_d0.934369
X-RAY DIFFRACTIONf_chiral_restr0.0487485
X-RAY DIFFRACTIONf_plane_restr0.0087579
X-RAY DIFFRACTIONf_dihedral_angle_d8.3192475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.31111360.26752619X-RAY DIFFRACTION99.96
2.06-2.130.28521370.2372620X-RAY DIFFRACTION100
2.13-2.20.2351170.22352648X-RAY DIFFRACTION100
2.2-2.290.28491430.23792616X-RAY DIFFRACTION100
2.29-2.390.26641450.20152622X-RAY DIFFRACTION100
2.39-2.520.25721480.20252644X-RAY DIFFRACTION100
2.52-2.680.22671320.1972641X-RAY DIFFRACTION99.93
2.68-2.880.22931410.19532662X-RAY DIFFRACTION100
2.88-3.170.26681270.2042687X-RAY DIFFRACTION100
3.17-3.630.22421510.18352671X-RAY DIFFRACTION100
3.63-4.560.18581430.14682708X-RAY DIFFRACTION99.86
4.56-19.470.18981300.15412851X-RAY DIFFRACTION99.93

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