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- PDB-8jno: Crystal structure of cytochrome P450 IkaD from Streptomyces sp. Z... -

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Basic information

Entry
Database: PDB / ID: 8jno
TitleCrystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate 10-epi-deOH-HSAF
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / hydroxylation / polycyclic tetramate macrolactam / cytochrome P450
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-E8T / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces sp. ZJ306 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Y.L. / 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 22, 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)94,0237
Polymers91,7742
Non-polymers2,2495
Water15,979887
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0234
Polymers45,8871
Non-polymers1,1363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area16300 Å2
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0003
Polymers45,8871
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-26 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.032, 82.178, 144.422
Angle α, β, γ (deg.)90.00, 94.32, 90.00
Int Tables number5
Space group name H-MI121
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-996-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 45887.109 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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-E8T / (1Z,3E,5S,7S,8R,9S,10S,11R,13R,15R,16S,18Z,25S)-11-ethyl-2,7-dihydroxy-10-methyl-21,26-diazapentacyclo[23.2.1.09,13.08,15.05,16]octacosa-1(2),3,18-triene-20,27,28-trione / 10-epi-deOH-HSAF


Mass: 496.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H40N2O5 / 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.: 887 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 3.5-4 M 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: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→12.91 Å / Num. obs: 70089 / % possible obs: 96.7 % / Redundancy: 9.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.121 / Χ2: 1.1 / Net I/σ(I): 14 / Num. measured all: 657390
Reflection shellResolution: 2→2.04 Å / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.273 / Num. measured all: 21841 / Num. unique obs: 4645 / CC1/2: 0.931 / Rpim(I) all: 0.139 / Rrim(I) all: 0.307 / Χ2: 0.71 / Net I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
AimlessCCP4Interface 7.0.073data scaling
CrysalisPro171.39.7edata reduction
MOLREPCCP4Interface 7.0.073phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→12.91 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 3467 5.06 %
Rwork0.2144 --
obs0.2171 68585 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→12.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 159 887 7106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126389
X-RAY DIFFRACTIONf_angle_d1.2868733
X-RAY DIFFRACTIONf_dihedral_angle_d8.102942
X-RAY DIFFRACTIONf_chiral_restr0.058957
X-RAY DIFFRACTIONf_plane_restr0.0131150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.29631620.2182706X-RAY DIFFRACTION100
2.03-2.060.26161550.21112736X-RAY DIFFRACTION100
2.06-2.090.28251520.20782720X-RAY DIFFRACTION100
2.09-2.120.28771470.20582727X-RAY DIFFRACTION100
2.12-2.150.29741340.23682735X-RAY DIFFRACTION100
2.15-2.190.91191100.65642170X-RAY DIFFRACTION79
2.19-2.230.47691120.40412377X-RAY DIFFRACTION87
2.23-2.270.44231420.39262688X-RAY DIFFRACTION98
2.27-2.320.4799100.3054352X-RAY DIFFRACTION13
2.32-2.370.27531390.22522761X-RAY DIFFRACTION100
2.37-2.420.27241330.16962734X-RAY DIFFRACTION100
2.42-2.480.22471350.182752X-RAY DIFFRACTION100
2.48-2.550.24021450.17812724X-RAY DIFFRACTION100
2.55-2.630.25831710.19012716X-RAY DIFFRACTION100
2.63-2.710.27491440.20072757X-RAY DIFFRACTION100
2.71-2.810.26721350.20952757X-RAY DIFFRACTION100
2.81-2.920.26531360.20622725X-RAY DIFFRACTION100
2.92-3.050.26831610.20842735X-RAY DIFFRACTION100
3.05-3.210.23891560.19932721X-RAY DIFFRACTION100
3.21-3.40.23251440.18862766X-RAY DIFFRACTION100
3.4-3.660.22711460.1882677X-RAY DIFFRACTION98
3.66-4.020.21211360.17022774X-RAY DIFFRACTION99
4.02-4.580.20481450.15162749X-RAY DIFFRACTION99
4.58-5.680.1891530.16152765X-RAY DIFFRACTION100
5.68-12.910.20341640.18572794X-RAY DIFFRACTION100

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