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- PDB-8jua: Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp.... -

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Basic information

Entry
Database: PDB / ID: 8jua
TitleMultifunctional cytochrome P450 enzyme IkaD from Streptomyces sp. ZJ306, in complex with epoxyikarugamycin
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / C-H functionalization / regioselectivity / chemoselectivity / polycyclic tetramate macrolactam (PoTeM) / cytochrome P450 enzyme
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
Chem-F7Z / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces sp. ZJ306 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.00001111553 Å
AuthorsZhang, Y.L. / Zhang, L.P. / Zhang, C.S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22193072 China
National Natural Science Foundation of China (NSFC)22177118 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 26, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,70714
Polymers96,1172
Non-polymers2,59012
Water13,457747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-8 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.6201, 81.9395, 144.165
Angle α, β, γ (deg.)90.0, 94.3858, 90.0
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-889-

HOH

21A-944-

HOH

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Components

#1: Protein Cytochrome P450 /


Mass: 48058.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. ZJ306 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4ZV78
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-F7Z / (1Z,3E,5S,7R,8R,10R,11R,12S,13R,15S,16R,17S,19Z,26S)-11-ethyl-2-hydroxy-10-methyl-22,27-diaza-14 oxahexacyclo[24.2.1.05,17.07,16.013,15.08,12]nonacosa-1(2),3,19-triene-21,28,29-trione / epoxyikarugamycin


Mass: 494.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H38N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 3.5-4M sodium formate

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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: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→23.310357633 Å / Num. obs: 72440 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.6584059616 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.049 / Rrim(I) all: 0.115 / Χ2: 0.98 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.04 Å / % possible obs: 99.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.638 / Num. measured all: 13298 / Num. unique obs: 4397 / CC1/2: 0.544 / Rpim(I) all: 0.432 / Rrim(I) all: 0.775 / Χ2: 0.95 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
AimlessCCP4Interface 7.1.015data scaling
CrysalisProCrysalisPro171.39.7edata reduction
MOLREPCCP4Interface 7.1.015phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.00001111553→23.310357633 Å / SU ML: 0.266269390977 / Cross valid method: FREE R-VALUE / σ(F): 1.33702057403 / Phase error: 26.2912515827
RfactorNum. reflection% reflection
Rfree0.255652344084 3659 5.05177412674 %
Rwork0.203840751972 68771 -
obs0.206499818957 72430 99.7054126975 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.6442843374 Å2
Refinement stepCycle: LAST / Resolution: 2.00001111553→23.310357633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6093 0 182 747 7022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01400286089766450
X-RAY DIFFRACTIONf_angle_d1.47340668638804
X-RAY DIFFRACTIONf_chiral_restr0.292470168004961
X-RAY DIFFRACTIONf_plane_restr0.008282463469571158
X-RAY DIFFRACTIONf_dihedral_angle_d14.84107224062410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00001111553-2.02630.3049951401521460.2659194873672612X-RAY DIFFRACTION99.3158084264
2.0263-2.05410.3088075839241490.259351540412622X-RAY DIFFRACTION99.6762589928
2.0541-2.08340.324930338531490.2550575072452600X-RAY DIFFRACTION99.8547039593
2.0834-2.11450.3393049728991420.2478790613412653X-RAY DIFFRACTION99.8927805575
2.1145-2.14750.3105774205111290.2548310700452641X-RAY DIFFRACTION99.8918139199
2.1475-2.18270.3014547307951380.2424687336452630X-RAY DIFFRACTION99.8556998557
2.1827-2.22030.3140478825281460.2371509936722626X-RAY DIFFRACTION100
2.2203-2.26060.2780653687921200.2227237083112670X-RAY DIFFRACTION100
2.2606-2.30410.2819221549831530.2256590004182650X-RAY DIFFRACTION100
2.3041-2.3510.3040746968651260.2212093114312653X-RAY DIFFRACTION100
2.351-2.40210.2772551607531230.209717184182648X-RAY DIFFRACTION99.9639249639
2.4021-2.45790.2850989150721390.1992026317912630X-RAY DIFFRACTION99.963898917
2.4579-2.51930.2287788619391440.1994931249252640X-RAY DIFFRACTION99.928212491
2.5193-2.58740.2675934811291420.1985336076122649X-RAY DIFFRACTION99.9283924096
2.5874-2.66340.2628003588771510.2030171097622630X-RAY DIFFRACTION99.928135106
2.6634-2.74920.2837883114381410.2056526532192659X-RAY DIFFRACTION99.9642984648
2.7492-2.84730.2832968992431270.2274760151522649X-RAY DIFFRACTION99.9280057595
2.8473-2.96110.2948163950821410.2334582055182693X-RAY DIFFRACTION99.859055673
2.9611-3.09560.2807605577841550.2296454923192614X-RAY DIFFRACTION99.8917748918
3.0956-3.25840.2709746332191510.2069123368472637X-RAY DIFFRACTION99.5003568879
3.2584-3.46190.2469395774021370.1939889877992635X-RAY DIFFRACTION99.7122302158
3.4619-3.72820.1908889826081410.1802754580992658X-RAY DIFFRACTION99.644001424
3.7282-4.10160.239959942651290.172318787032664X-RAY DIFFRACTION99.2184724689
4.1016-4.69090.2166371037371450.1621118295182621X-RAY DIFFRACTION98.5042735043
4.6909-5.89420.2057555125251370.1696662571292678X-RAY DIFFRACTION99.0499648135
5.8942-23.3103576330.1847527630231580.1789565824342709X-RAY DIFFRACTION99.0328151986
Refinement TLS params.Method: refined / Origin x: -2.81231770447 Å / Origin y: 0.375290560333 Å / Origin z: 25.3174487241 Å
111213212223313233
T-0.147272190118 Å20.129662770995 Å2-0.0138499679173 Å2--0.157675758099 Å20.0138320782461 Å2---0.0104175351856 Å2
L0.0275107612743 °2-0.00314927791305 °2-0.000529576860111 °2-0.0332860655389 °2-0.0115149624331 °2--0.0385869672329 °2
S-0.153963891059 Å °0.0456533862544 Å °-0.0257987939365 Å °0.0969743509789 Å °0.0182330311699 Å °-0.00107561510074 Å °0.000485535888523 Å °-0.0271653993526 Å °-4.91156709957E-12 Å °
Refinement TLS groupSelection details: all

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