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- PDB-8dsg: P411-PFA carbene transferase -

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Basic information

Entry
Database: PDB / ID: 8dsg
TitleP411-PFA carbene transferase
ComponentsCytochrome P450-BM3 variant P411-PFA
KeywordsOXIDOREDUCTASE / cytochrome P450 / carbene transferase / cyanomethylase / fluoroalkylation
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMaggiolo, A.O. / Porter, N.J. / Zhang, J. / Arnold, F.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138740 United States
CitationJournal: Nat Catal / Year: 2023
Title: Chemodivergent C(sp 3 )-H and C(sp 2 )-H Cyanomethylation Using Engineered Carbene Transferases.
Authors: Zhang, J. / Maggiolo, A.O. / Alfonzo, E. / Mao, R. / Porter, N.J. / Abney, N. / Arnold, F.H.
History
DepositionJul 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450-BM3 variant P411-PFA
B: Cytochrome P450-BM3 variant P411-PFA
C: Cytochrome P450-BM3 variant P411-PFA
D: Cytochrome P450-BM3 variant P411-PFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,84125
Polymers215,8224
Non-polymers4,01921
Water17,745985
1
A: Cytochrome P450-BM3 variant P411-PFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0977
Polymers53,9551
Non-polymers1,1426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450-BM3 variant P411-PFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0637
Polymers53,9551
Non-polymers1,1086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450-BM3 variant P411-PFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7925
Polymers53,9551
Non-polymers8374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450-BM3 variant P411-PFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8886
Polymers53,9551
Non-polymers9335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.254, 172.462, 225.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome P450-BM3 variant P411-PFA


Mass: 53955.488 Da / Num. of mol.: 4
Mutation: N71T, A75G, V79L, A83L, F88A, M119S, P143S, T176I, A185V, S227T, H237Q, E253G, I264Y, H267V, T269G, A291V, T328V, A329V, A331V, L354V, I367V, C401S, I402P, T437L, L438Q, E443K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: F2Q7T0, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 5 types, 1006 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 mM ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 147073 / % possible obs: 91.8 % / Redundancy: 2.4 % / Rpim(I) all: 0.056 / Net I/σ(I): 21.6
Reflection shellResolution: 1.87→1.9 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5709 / Rpim(I) all: 0.282

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UCW

5ucw


Resolution: 1.87→38.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.427 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21795 7853 5.1 %RANDOM
Rwork0.18723 ---
obs0.18882 147073 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.043 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.87→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14486 0 266 985 15737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01315341
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714689
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.66820807
X-RAY DIFFRACTIONr_angle_other_deg1.1321.59533935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01251848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69823.168808
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.953152755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.651585
X-RAY DIFFRACTIONr_chiral_restr0.0540.21885
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217257
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023465
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7512.1547311
X-RAY DIFFRACTIONr_mcbond_other0.7512.1547310
X-RAY DIFFRACTIONr_mcangle_it1.313.2199168
X-RAY DIFFRACTIONr_mcangle_other1.313.2199169
X-RAY DIFFRACTIONr_scbond_it0.7322.258030
X-RAY DIFFRACTIONr_scbond_other0.7322.2458023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2473.33211622
X-RAY DIFFRACTIONr_long_range_B_refined3.17724.79817014
X-RAY DIFFRACTIONr_long_range_B_other3.02224.58716837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.917 Å
RfactorNum. reflection% reflection
Rfree0.289 290 -
Rwork0.257 5709 -
obs--48.39 %

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