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- PDB-7ttp: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation -

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Basic information

Entry
Database: PDB / ID: 7ttp
TitleP450 (OxyA) from kistamicin biosynthesis, mixed heme conformation
Componentscytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / peptide cyclase / NRPS-associated / glycopeptide antibiotic
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Putative cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesActinomadura parvosata subsp. kistnae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGreule, A. / Izore, T. / Cryle, M.J.
Funding support Australia, Germany, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1140619 Australia
Australian Research Council (ARC)DP170102220 Australia
German Research Foundation (DFG)CR 392/1-1 Germany
CitationJournal: Front Chem / Year: 2022
Title: The Cytochrome P450 OxyA from the Kistamicin Biosynthesis Cyclization Cascade is Highly Sensitive to Oxidative Damage.
Authors: Greule, A. / Izore, T. / Machell, D. / Hansen, M.H. / Schoppet, M. / De Voss, J.J. / Charkoudian, L.K. / Schittenhelm, R.B. / Harmer, J.R. / Cryle, M.J.
History
DepositionFeb 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: 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 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4873
Polymers42,7781
Non-polymers7092
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-28 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.806, 69.806, 132.456
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

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Components

#1: Protein cytochrome P450 hydroxylase


Mass: 42778.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura parvosata subsp. kistnae (bacteria)
Gene: KIS93_04812 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress / References: UniProt: A0A2P9IBF7, Oxidoreductases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT, pH 6.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.799→35.66 Å / Num. obs: 33365 / % possible obs: 94 % / Redundancy: 2 % / Biso Wilson estimate: 24.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02083 / Rrim(I) all: 0.02946 / Net I/σ(I): 23.4
Reflection shellResolution: 1.799→1.863 Å / Redundancy: 2 % / Rmerge(I) obs: 0.0262 / Num. unique obs: 3340 / CC1/2: 0.851 / Rrim(I) all: 0.3706 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHYRE Model

Resolution: 1.8→35.66 Å / SU ML: 0.2279 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 1574 4.72 %
Rwork0.1854 31791 -
obs0.1869 33365 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 49 217 2932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092780
X-RAY DIFFRACTIONf_angle_d0.88563781
X-RAY DIFFRACTIONf_chiral_restr0.0482423
X-RAY DIFFRACTIONf_plane_restr0.0087493
X-RAY DIFFRACTIONf_dihedral_angle_d13.77921036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.33611360.29252871X-RAY DIFFRACTION96.25
1.86-1.920.29151400.25592969X-RAY DIFFRACTION96.49
1.92-20.27111250.22312918X-RAY DIFFRACTION96.27
2-2.090.2331700.1992868X-RAY DIFFRACTION95.93
2.09-2.20.23191500.19552901X-RAY DIFFRACTION95.58
2.2-2.340.22261620.19992886X-RAY DIFFRACTION94.98
2.34-2.520.21681290.17392874X-RAY DIFFRACTION94.26
2.52-2.770.22841490.18612852X-RAY DIFFRACTION93.55
2.78-3.170.22121570.18342871X-RAY DIFFRACTION93.23
3.18-40.18951360.16542857X-RAY DIFFRACTION91.75
4-35.660.19561200.16862924X-RAY DIFFRACTION88.64

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