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- PDB-6f0b: Cytochrome P450 TxtC employs substrate conformational switching f... -

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Basic information

Entry
Database: PDB / ID: 6f0b
TitleCytochrome P450 TxtC employs substrate conformational switching for sequential aliphatic and aromatic thaxtomin hydroxylation
ComponentsCytochrome P450 monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / TxtC / Thaxtomin hydroxylation
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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C8H / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces acidiscabies 84-104 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFulop, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H006281/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Binding of Distinct Substrate Conformations Enables Hydroxylation of Remote Sites in Thaxtomin D by Cytochrome P450 TxtC.
Authors: Alkhalaf, L.M. / Barry, S.M. / Rea, D. / Gallo, A. / Griffiths, D. / Lewandowski, J.R. / Fulop, V. / Challis, G.L.
History
DepositionNov 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4943
Polymers43,4711
Non-polymers1,0232
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-24 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.780, 84.240, 86.270
Angle α, β, γ (deg.)90.00, 135.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytochrome P450 monooxygenase / Cytochrome P450-SU2


Mass: 43471.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces acidiscabies 84-104 (bacteria)
Gene: txtC, a10_01524 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q8VS75
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-C8H / (3~{S},6~{S})-1,4-dimethyl-3-[(4-nitro-1~{H}-indol-3-yl)methyl]-6-(phenylmethyl)piperazine-2,5-dione


Mass: 406.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaF, 20% PEG 3350, 0.1 M Bis-Tris propane / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012 / Details: MIRROR
RadiationMonochromator: MIROOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. obs: 14147 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 80.7 Å2 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.07 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2 / Num. unique obs: 1023 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z36

2z36


Resolution: 2.8→34.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 25.247 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.777 / ESU R Free: 0.311 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22799 599 4.2 %RANDOM
Rwork0.17642 ---
obs0.17866 13548 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.501 Å2
Baniso -1Baniso -2Baniso -3
1--4.26 Å2-0 Å2-2.61 Å2
2--12.09 Å20 Å2
3----1.72 Å2
Refinement stepCycle: 1 / Resolution: 2.8→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 73 14 3061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193129
X-RAY DIFFRACTIONr_bond_other_d0.0020.022978
X-RAY DIFFRACTIONr_angle_refined_deg1.7942.0134285
X-RAY DIFFRACTIONr_angle_other_deg0.92936841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97622.941136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79515484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8361529
X-RAY DIFFRACTIONr_chiral_restr0.0970.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213541
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02703
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 52 -
Rwork0.291 971 -
obs--94.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0620.3621-0.39431.2019-0.51971.1598-0.0147-0.0345-0.1029-0.0231-0.0413-0.0602-0.0324-0.05690.0560.9190.0408-0.1290.0209-0.03390.9-35.786-2.1375.326
22.27670.5-0.4821.25180.82111.6231-0.13110.29910.0857-0.13850.15870.1962-0.0623-0.1292-0.02770.92780.0471-0.1860.11120.02860.9346-47.7072.532-6.831
31.79210.3964-0.78820.5874-0.6141.56850.0122-0.2141-0.2145-0.0087-0.1631-0.1989-0.02010.17630.15090.94860.0618-0.10680.05840.00750.9767-24.548-3.2119.036
40.55050.45280.26442.124-0.2641.2643-0.0926-0.0059-0.0584-0.1023-0.0497-0.06-0.09530.1740.14230.96570.0202-0.09680.0308-0.01620.957-24.5424.3481.647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 148
2X-RAY DIFFRACTION2A149 - 231
3X-RAY DIFFRACTION3A232 - 329
4X-RAY DIFFRACTION4A330 - 395

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