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

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Basic information

Entry
Database: PDB / ID: 8jnc
TitleCrystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate 10-epi-maltophilin
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-E5I / FORMIC ACID / 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 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)94,23611
Polymers91,7742
Non-polymers2,4619
Water15,259847
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1065
Polymers45,8871
Non-polymers1,2194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-26 kcal/mol
Surface area16170 Å2
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1296
Polymers45,8871
Non-polymers1,2425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.895, 81.948, 143.838
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-910-

HOH

21A-1005-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 856 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-E5I / (1Z,3E,5S,8R,9S,10S,11R,13R,15R,16S,18Z,24S,25S)-11-ethyl-2,24-dihydroxy-10-methyl-21,26-diazapentacyclo[23.2.1.09,13.08,15.05,16]octacosa-1(2),3,18-triene-7,20,27,28-tetraone / 10-Epi-maltophilin


Mass: 510.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H38N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.94 Å3/Da / Density % sol: 58.2 %
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: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→13.29 Å / Num. obs: 71321 / % possible obs: 99.2 % / Redundancy: 4.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.08 / Rrim(I) all: 0.182 / Χ2: 0.92 / Net I/σ(I): 7.8 / Num. measured all: 351712
Reflection shellResolution: 2→2.04 Å / % possible obs: 97.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.647 / Num. measured all: 12301 / Num. unique obs: 4530 / CC1/2: 0.538 / Rpim(I) all: 0.463 / Rrim(I) all: 0.801 / Χ2: 0.79 / Net I/σ(I) obs: 1.5

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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→13.29 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 3618 5.07 %
Rwork0.189 --
obs0.1912 71307 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→13.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6098 0 173 847 7118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126439
X-RAY DIFFRACTIONf_angle_d1.3358792
X-RAY DIFFRACTIONf_dihedral_angle_d8.264947
X-RAY DIFFRACTIONf_chiral_restr0.059958
X-RAY DIFFRACTIONf_plane_restr0.0111156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.2971550.24682500X-RAY DIFFRACTION97
2.03-2.050.29071450.24892552X-RAY DIFFRACTION98
2.05-2.080.29411470.23552528X-RAY DIFFRACTION98
2.08-2.110.28961340.22532597X-RAY DIFFRACTION99
2.11-2.150.26131260.21922589X-RAY DIFFRACTION99
2.15-2.180.26611340.20712594X-RAY DIFFRACTION99
2.18-2.220.25441340.19942584X-RAY DIFFRACTION100
2.22-2.260.2291350.19412640X-RAY DIFFRACTION100
2.26-2.30.261470.19122603X-RAY DIFFRACTION100
2.3-2.350.21571230.18942632X-RAY DIFFRACTION100
2.35-2.40.25561210.19052605X-RAY DIFFRACTION100
2.4-2.460.2551340.18012612X-RAY DIFFRACTION100
2.46-2.520.23811420.18332611X-RAY DIFFRACTION100
2.52-2.580.25061370.18742599X-RAY DIFFRACTION100
2.58-2.660.24031560.19372613X-RAY DIFFRACTION100
2.66-2.750.27971370.20632619X-RAY DIFFRACTION100
2.75-2.840.29451250.20722654X-RAY DIFFRACTION100
2.84-2.950.29891410.21182616X-RAY DIFFRACTION100
2.96-3.090.22811540.21322581X-RAY DIFFRACTION100
3.09-3.250.2631490.19552625X-RAY DIFFRACTION100
3.25-3.450.21431350.17632625X-RAY DIFFRACTION100
3.45-3.710.16631380.16652617X-RAY DIFFRACTION100
3.71-4.070.18471310.15222622X-RAY DIFFRACTION100
4.07-4.640.19191430.1462647X-RAY DIFFRACTION99
4.64-5.760.17991370.16122625X-RAY DIFFRACTION99
5.77-13.290.18541580.1832599X-RAY DIFFRACTION97

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