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- PDB-7xbm: Crystal Structure of cytochrome P450 PikC with the unnatural amin... -

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Basic information

Entry
Database: PDB / ID: 7xbm
TitleCrystal Structure of cytochrome P450 PikC with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238
ComponentsCytochrome P450 monooxygenase PikC
KeywordsOXIDOREDUCTASE / unnatural amino acid
Function / homology
Function and homology information


pikromycin synthase / macrolide biosynthetic process / 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
CACODYLATE ION / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, G.B. / Pan, Y.J. / Li, S.Y. / Gao, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000039 China
National Natural Science Foundation of China (NSFC)32025001 China
National Natural Science Foundation of China (NSFC)31872729 China
CitationJournal: Nat Commun / Year: 2023
Title: Crystal Structure of cytochrome P450 PikC with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238
Authors: Pan, Y.J. / Li, G.B. / Gao, X. / Li, S.Y.
History
DepositionMar 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,32017
Polymers98,7822
Non-polymers2,53815
Water6,936385
1
A: Cytochrome P450 monooxygenase PikC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5177
Polymers49,3911
Non-polymers1,1266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 monooxygenase PikC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,80310
Polymers49,3911
Non-polymers1,4129
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.040, 108.331, 153.300
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

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 monooxygenase PikC / Cytochrome P450 monooxygenase PicK / Narbomycin C-12 hydroxylase / Pikromycin synthase CYP107L1


Mass: 49390.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: pikC, picK / Production host: Escherichia coli (E. coli) / References: UniProt: O87605, pikromycin synthase

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Non-polymers , 6 types, 400 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M Li2SO4, 0.1M sodium cacodylate, pH6.1, 16% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 39557 / % possible obs: 99.5 % / Redundancy: 12.4 % / Biso Wilson estimate: 34.67 Å2 / CC1/2: 1 / Net I/σ(I): 24.5
Reflection shellResolution: 2.4→2.5 Å / Num. unique obs: 3737 / CC1/2: 0.882

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVJ

2bvj


Resolution: 2.4→23.51 Å / SU ML: 0.2861 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 2000 5.44 %
Rwork0.1838 34758 -
obs0.1863 36758 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→23.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6150 0 162 385 6697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236457
X-RAY DIFFRACTIONf_angle_d0.5338816
X-RAY DIFFRACTIONf_chiral_restr0.0396964
X-RAY DIFFRACTIONf_plane_restr0.00451148
X-RAY DIFFRACTIONf_dihedral_angle_d15.13912409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.2995930.22581629X-RAY DIFFRACTION62.44
2.46-2.530.31611100.22851897X-RAY DIFFRACTION71.4
2.53-2.610.26141210.2222114X-RAY DIFFRACTION80.11
2.61-2.690.30941340.22992331X-RAY DIFFRACTION88.64
2.69-2.790.27081460.23322537X-RAY DIFFRACTION96.23
2.79-2.90.28091520.22592634X-RAY DIFFRACTION99.39
2.9-3.030.26981530.21942662X-RAY DIFFRACTION99.96
3.03-3.190.2731520.20362652X-RAY DIFFRACTION100
3.19-3.390.20481530.19192663X-RAY DIFFRACTION99.96
3.39-3.650.27521540.18082673X-RAY DIFFRACTION100
3.65-4.010.20791560.15652703X-RAY DIFFRACTION99.97
4.01-4.590.17071550.14512698X-RAY DIFFRACTION99.96
4.59-5.770.20491560.16382732X-RAY DIFFRACTION100
5.77-23.510.19371650.17132833X-RAY DIFFRACTION98.94

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