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- PDB-8gue: Crystal Structure of narbomycin-bound cytochrome P450 PikC with t... -

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Basic information

Entry
Database: PDB / ID: 8gue
TitleCrystal Structure of narbomycin-bound cytochrome P450 PikC with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238
ComponentsCytochrome P450 monooxygenase PikC
KeywordsOXIDOREDUCTASE / Narbomycin-bound / PikC / unnatural amino acid
Function / homology
Function and homology information


pikromycin synthase / macrolide biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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
PROTOPORPHYRIN IX CONTAINING FE / NARBOMYCIN / DI(HYDROXYETHYL)ETHER / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Unnatural activities and mechanistic insights of cytochrome P450 PikC gained from site-specific mutagenesis by non-canonical amino acids.
Authors: Pan, Y. / Li, G. / Liu, R. / Guo, J. / Liu, Y. / Liu, M. / Zhang, X. / Chi, L. / Xu, K. / Wu, R. / Zhang, Y. / Li, Y. / Gao, X. / Li, S.
History
DepositionSep 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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 ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _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)98,20722
Polymers94,4392
Non-polymers3,76820
Water5,423301
1
A: Cytochrome P450 monooxygenase PikC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,24612
Polymers47,2201
Non-polymers2,02711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-21 kcal/mol
Surface area16470 Å2
MethodPISA
2
B: Cytochrome P450 monooxygenase PikC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,96010
Polymers47,2201
Non-polymers1,7419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-21 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.465, 97.818, 141.075
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: 47219.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238
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 , 7 types, 321 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-NRB / NARBOMYCIN


Mass: 509.675 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H47NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Li2SO4, 0.1 M Bis-Tris, pH6.0, 18% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 65500 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 33.16 Å2 / CC1/2: 0.994 / Net I/σ(I): 15.75
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 6460 / CC1/2: 0.71

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Processing

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

2bvj


Resolution: 1.9→37.77 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2504 1999 3.06 %
Rwork0.201 63379 -
obs0.2025 65378 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.41 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 243 301 6672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516515
X-RAY DIFFRACTIONf_angle_d0.80388916
X-RAY DIFFRACTIONf_chiral_restr0.0473984
X-RAY DIFFRACTIONf_plane_restr0.00731153
X-RAY DIFFRACTIONf_dihedral_angle_d9.3177930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.33661360.30514295X-RAY DIFFRACTION95.52
1.95-20.30691400.26744467X-RAY DIFFRACTION99.96
2-2.060.31321420.24654477X-RAY DIFFRACTION100
2.06-2.130.25431420.22234509X-RAY DIFFRACTION99.96
2.13-2.20.26731420.2074503X-RAY DIFFRACTION100
2.2-2.290.27171420.20624495X-RAY DIFFRACTION99.94
2.29-2.390.26981420.21214503X-RAY DIFFRACTION100
2.39-2.520.23881420.2024498X-RAY DIFFRACTION99.98
2.52-2.680.28991430.21684533X-RAY DIFFRACTION99.98
2.68-2.880.28311440.21864542X-RAY DIFFRACTION99.94
2.88-3.170.26411430.21234554X-RAY DIFFRACTION99.96
3.18-3.630.25471440.18924570X-RAY DIFFRACTION99.98
3.63-4.580.19381460.17114630X-RAY DIFFRACTION99.92
4.58-37.770.23741510.18964803X-RAY DIFFRACTION99.68

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