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- PDB-7ttq: P450 (OxyA) from kistamicin biosynthesis, imidazole complex -

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Basic information

Entry
Database: PDB / ID: 7ttq
TitleP450 (OxyA) from kistamicin biosynthesis, imidazole complex
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 / IMIDAZOLE / Putative cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesActinomadura parvosata subsp. kistnae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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)43,5564
Polymers42,7781
Non-polymers7783
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-24 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.659, 69.659, 132.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT, pH 6.0, 25% PEG1500, 2 mM imidazole

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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: 1.62→44.582 Å / Num. obs: 45953 / % possible obs: 99 % / Redundancy: 10.8 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Χ2: 0.94 / Net I/σ(I): 17.7
Reflection shellResolution: 1.638→1.696 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4024 / CC1/2: 0.304 / Rpim(I) all: 0.743 / Χ2: 0.6

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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: 1.62→44.58 Å / SU ML: 0.168 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 2285 4.97 %
Rwork0.1779 43666 -
obs0.1793 45951 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.71 Å2
Refinement stepCycle: LAST / Resolution: 1.62→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 54 221 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982903
X-RAY DIFFRACTIONf_angle_d1.05363959
X-RAY DIFFRACTIONf_chiral_restr0.0553446
X-RAY DIFFRACTIONf_plane_restr0.01518
X-RAY DIFFRACTIONf_dihedral_angle_d13.09891093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.2637480.2824886X-RAY DIFFRACTION31.76
1.66-1.690.26981240.23272830X-RAY DIFFRACTION100
1.69-1.740.24651370.21792831X-RAY DIFFRACTION100
1.74-1.780.26411260.19782822X-RAY DIFFRACTION99.97
1.78-1.840.22231430.19772817X-RAY DIFFRACTION99.97
1.84-1.90.24221660.19592781X-RAY DIFFRACTION99.93
1.9-1.960.24671230.21332842X-RAY DIFFRACTION100
1.96-2.040.20721510.18512854X-RAY DIFFRACTION100
2.04-2.130.19991390.17912837X-RAY DIFFRACTION100
2.13-2.250.22081350.16472854X-RAY DIFFRACTION100
2.25-2.390.18861480.17742828X-RAY DIFFRACTION99.97
2.39-2.570.20681610.16972843X-RAY DIFFRACTION100
2.57-2.830.22241960.1752808X-RAY DIFFRACTION99.97
2.83-3.240.17231580.1662884X-RAY DIFFRACTION99.97
3.24-4.080.17811650.1552906X-RAY DIFFRACTION99.97
4.08-44.580.20031650.18413043X-RAY DIFFRACTION99.72

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