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- PDB-7ttb: P450 (OxyA) from kistamicin biosynthesis, Y99F mutant -

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Basic information

Entry
Database: PDB / ID: 7ttb
TitleP450 (OxyA) from kistamicin biosynthesis, Y99F mutant
ComponentsPutative cytochrome 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: 1.80159202452 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: Putative cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4713
Polymers42,7621
Non-polymers7092
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-26 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.801, 69.801, 132.356
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 Putative cytochrome P450 hydroxylase


Mass: 42762.207 Da / Num. of mol.: 1 / Mutation: Y99F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura parvosata subsp. kistnae (bacteria)
Gene: KIS93_04812 / Production host: Escherichia coli BL1 (bacteria) / Strain (production host): ArticExpress / References: UniProt: A0A2P9IBF7
#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.: 168 / 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: 2.37 Å3/Da / Density % sol: 43.49 %
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: 1.8→44.63 Å / Num. obs: 35272 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 26.0371633274 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.027 / Rrim(I) all: 0.063 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2053 / CC1/2: 0.657 / Rpim(I) all: 0.422 / Rrim(I) all: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHYRE Model

Resolution: 1.80159202452→35.6367186788 Å / SU ML: 0.219280613419 / Cross valid method: FREE R-VALUE / σ(F): 1.34350040492 / Phase error: 22.0568449204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223911407816 1679 4.76704238948 %
Rwork0.184039624568 33542 -
obs0.185905701289 35221 99.8922260983 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.9332473469 Å2
Refinement stepCycle: LAST / Resolution: 1.80159202452→35.6367186788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 49 168 2949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471995809013005
X-RAY DIFFRACTIONf_angle_d0.7790198834112
X-RAY DIFFRACTIONf_chiral_restr0.0417846482138449
X-RAY DIFFRACTIONf_plane_restr0.00428236133013538
X-RAY DIFFRACTIONf_dihedral_angle_d18.64273071611810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8016-1.85460.3187511431381410.2692512481782730X-RAY DIFFRACTION99.6875
1.8546-1.91450.3113446710451330.243092504532763X-RAY DIFFRACTION100
1.9145-1.98290.3113054308871240.2317196993352773X-RAY DIFFRACTION99.9310106933
1.9829-2.06230.2387430638391440.2113251868712758X-RAY DIFFRACTION100
2.0623-2.15610.2501374818561560.1979136523942746X-RAY DIFFRACTION100
2.1561-2.26980.2294796553641360.1844250007682777X-RAY DIFFRACTION99.9656829101
2.2698-2.41190.2314661874531550.1849856921782766X-RAY DIFFRACTION99.8974008208
2.4119-2.59810.2428959454381280.1825125008682795X-RAY DIFFRACTION100
2.5981-2.85950.2246856368781460.1909248078632774X-RAY DIFFRACTION100
2.8595-3.2730.2246359721871510.1949846589942812X-RAY DIFFRACTION99.9662618084
3.273-4.12270.1925838000221330.16276355862866X-RAY DIFFRACTION100
4.1227-35.6360.1922333075061320.16324892542982X-RAY DIFFRACTION99.3618379068

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