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

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Basic information

Entry
Database: PDB / ID: 8joo
TitleCrystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate ikarugamycin
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-EIA / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces sp. ZJ306 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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 8, 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)94,26413
Polymers91,7742
Non-polymers2,48911
Water11,584643
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1206
Polymers45,8871
Non-polymers1,2335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-25 kcal/mol
Surface area16160 Å2
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1437
Polymers45,8871
Non-polymers1,2566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-24 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.174, 82.121, 143.920
Angle α, β, γ (deg.)90.00, 94.41, 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-898-

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 (E. coli) / References: UniProt: A0A0B4ZV78

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Non-polymers , 5 types, 654 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-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.: 2 / Source method: obtained synthetically / Formula: C29H38N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: isolated from a natural source / 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.: 643 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 3.5-4.0 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: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.25→19.89 Å / Num. obs: 49517 / % possible obs: 97.5 % / Redundancy: 2.8 % / CC1/2: 0.977 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.108 / Rrim(I) all: 0.193 / Χ2: 1 / Net I/σ(I): 5 / Num. measured all: 139583
Reflection shellResolution: 2.25→2.32 Å / % possible obs: 98.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.418 / Num. measured all: 13314 / Num. unique obs: 4579 / CC1/2: 0.79 / Rpim(I) all: 0.282 / Rrim(I) all: 0.508 / Χ2: 0.9 / Net I/σ(I) obs: 2.3

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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: 2.25→19.89 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 2534 5.14 %
Rwork0.2166 --
obs0.2191 49325 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 175 643 6901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056425
X-RAY DIFFRACTIONf_angle_d0.8758769
X-RAY DIFFRACTIONf_dihedral_angle_d8.038944
X-RAY DIFFRACTIONf_chiral_restr0.043956
X-RAY DIFFRACTIONf_plane_restr0.0071158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.29281230.25412605X-RAY DIFFRACTION98
2.29-2.340.28731400.24832632X-RAY DIFFRACTION99
2.34-2.390.28911500.2352604X-RAY DIFFRACTION98
2.39-2.450.29371400.22922662X-RAY DIFFRACTION99
2.45-2.510.27431600.23592629X-RAY DIFFRACTION98
2.51-2.570.27751380.22132630X-RAY DIFFRACTION99
2.58-2.650.31731420.23312616X-RAY DIFFRACTION99
2.65-2.740.30251530.23712620X-RAY DIFFRACTION99
2.74-2.830.29231460.23842615X-RAY DIFFRACTION99
2.83-2.950.33121500.24472657X-RAY DIFFRACTION98
2.95-3.080.28931470.23292623X-RAY DIFFRACTION98
3.08-3.240.24691430.22072627X-RAY DIFFRACTION98
3.24-3.440.2471300.22052613X-RAY DIFFRACTION97
3.44-3.710.23451460.19882582X-RAY DIFFRACTION97
3.71-4.080.21841150.18932579X-RAY DIFFRACTION95
4.08-4.660.22781540.17272533X-RAY DIFFRACTION94
4.66-5.850.24251320.19262573X-RAY DIFFRACTION94
5.85-19.890.23591250.21142391X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: -2.8714 Å / Origin y: 0.479 Å / Origin z: 25.3596 Å
111213212223313233
T0.0931 Å20.0049 Å20.0006 Å2-0.0461 Å20.0055 Å2--0.0693 Å2
L0.8547 °2-0.0074 °20.0126 °2-0.5245 °20.0059 °2--0.7743 °2
S-0.0469 Å °0.029 Å °-0.0105 Å °0.0243 Å °0.0281 Å °0.0033 Å °-0.0172 Å °-0.0106 Å °0.014 Å °
Refinement TLS groupSelection details: all

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