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- PDB-6f0c: Cytochrome P450 TxtC employs substrate conformational switching f... -

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Basic information

Entry
Database: PDB / ID: 6f0c
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-C8B / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces acidiscabies 84-104 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5424
Polymers43,4711
Non-polymers1,0713
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-24 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.400, 84.500, 84.400
Angle α, β, γ (deg.)90.00, 133.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21A-815-

HOH

31A-893-

HOH

41A-929-

HOH

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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-C8B / (3~{R},6~{S})-1,4-dimethyl-6-[(4-nitro-1~{H}-indol-3-yl)methyl]-3-oxidanyl-3-(phenylmethyl)piperazine-2,5-dione


Mass: 422.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O5
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8000, 20% Ethylene Glycol, 0.03 M divalent cations, 0.1 M MOPS/HEPES
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2013 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→43 Å / Num. obs: 65551 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.89 % / Biso Wilson estimate: 32.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.04 / Net I/σ(I): 15.2
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / Num. unique obs: 4583 / CC1/2: 0.8 / Rrim(I) all: 0.56 / % possible all: 99.2

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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: 1.7→42.86 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.195 / SU ML: 0.058 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.076 / SU Rfree Cruickshank DPI: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18708 2701 4.1 %RANDOM
Rwork0.16158 ---
obs0.16261 62850 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20.88 Å2
2---1.47 Å2-0 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.7→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 76 446 3496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193131
X-RAY DIFFRACTIONr_bond_other_d0.0010.022977
X-RAY DIFFRACTIONr_angle_refined_deg1.7242.0144288
X-RAY DIFFRACTIONr_angle_other_deg0.87536838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96222.941136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24915484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7291529
X-RAY DIFFRACTIONr_chiral_restr0.1040.2478
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 208 -
Rwork0.274 4583 -
obs--99.01 %
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)
10.66910.42861.28592.6841.72762.99490.0859-0.2028-0.04790.3744-0.12490.02130.2759-0.3010.03910.4363-0.00650.04460.32870.02840.0645-1.39838.75652.67
20.55140.40130.13171.29050.43021.0024-0.0583-0.01520.0093-0.09350.0867-0.1052-0.09440.1544-0.02840.25330.04120.01750.22030.01630.05229.18345.56735.235
30.65570.54380.26421.13940.37930.6885-0.0588-0.0264-0.0171-0.12220.0223-0.0244-0.0285-0.02180.03640.28390.04010.01710.22970.01630.06263.48740.2332.19
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 31
2X-RAY DIFFRACTION2A32 - 133
3X-RAY DIFFRACTION3A134 - 395

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