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

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Basic information

Entry
Database: PDB / ID: 7tto
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: 1.6 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)43,3952
Polymers42,7781
Non-polymers6161
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-26 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.996, 69.996, 132.386
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
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: 1.599→44.705 Å / Num. obs: 50318 / % possible obs: 99.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 22.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Net I/σ(I): 24.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4 / Num. unique obs: 2374 / CC1/2: 0.938 / Rpim(I) all: 0.176 / Rrim(I) all: 0.57 / % possible all: 96.2

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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: 1.6→44.7 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 2484 4.96 %
Rwork0.1983 47583 -
obs0.1997 50067 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 43 229 3027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792945
X-RAY DIFFRACTIONf_angle_d2.62064030
X-RAY DIFFRACTIONf_chiral_restr0.0383444
X-RAY DIFFRACTIONf_plane_restr0.0048523
X-RAY DIFFRACTIONf_dihedral_angle_d12.78811128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.32921300.30032527X-RAY DIFFRACTION96.51
1.63-1.660.28531360.26912645X-RAY DIFFRACTION100
1.66-1.70.25681690.24792575X-RAY DIFFRACTION100
1.7-1.740.26351270.2432621X-RAY DIFFRACTION100
1.74-1.780.2391360.22962639X-RAY DIFFRACTION100
1.78-1.830.28771280.22162614X-RAY DIFFRACTION100
1.83-1.880.24231440.23312614X-RAY DIFFRACTION99.96
1.88-1.950.27421240.27192589X-RAY DIFFRACTION96.27
1.95-2.020.25881200.25082621X-RAY DIFFRACTION99.89
2.02-2.10.26521380.21832600X-RAY DIFFRACTION98.88
2.1-2.190.24431410.21132668X-RAY DIFFRACTION100
2.19-2.310.23831160.20472596X-RAY DIFFRACTION98.15
2.31-2.450.19661560.18532650X-RAY DIFFRACTION100
2.45-2.640.21741470.19492670X-RAY DIFFRACTION100
2.64-2.910.22881160.19982695X-RAY DIFFRACTION99.96
2.91-3.330.25811630.19432681X-RAY DIFFRACTION100
3.33-4.190.19041590.16882705X-RAY DIFFRACTION99.83
4.19-44.70.18511340.17092873X-RAY DIFFRACTION100

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