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

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Basic information

Entry
Database: PDB / ID: 7tta
TitleP450 (OxyA) from kistamicin biosynthesis, mixed heme conformation, attenuated beam
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: 2.001 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)43,0883
Polymers42,3801
Non-polymers7092
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-26 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.051, 70.051, 132.668
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative cytochrome P450 hydroxylase


Mass: 42379.688 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 BL21 (bacteria) / Strain (production host): ArcticExpress / References: UniProt: A0A2P9IBF7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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: 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: 2.4 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT, 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: 2.001→44.767 Å / Num. obs: 25756 / % possible obs: 99 % / Redundancy: 1.9 % / Biso Wilson estimate: 32.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05282 / Rrim(I) all: 0.0747 / Net I/σ(I): 8.1
Reflection shellResolution: 2.001→2.073 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.05282 / Num. unique obs: 4458 / CC1/2: 0.776 / Rrim(I) all: 0.6352 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHYRE Model

Resolution: 2.001→44.767 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1210 4.7 %
Rwork0.1978 --
obs0.1998 25738 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→44.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 49 229 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082918
X-RAY DIFFRACTIONf_angle_d2.5853985
X-RAY DIFFRACTIONf_dihedral_angle_d15.1631763
X-RAY DIFFRACTIONf_chiral_restr0.037438
X-RAY DIFFRACTIONf_plane_restr0.004516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.08080.3621080.31712596X-RAY DIFFRACTION96
2.0808-2.17550.31311320.26782716X-RAY DIFFRACTION99
2.1755-2.29010.30971450.27322627X-RAY DIFFRACTION98
2.2901-2.43360.30551180.2182743X-RAY DIFFRACTION99
2.4336-2.62150.2421270.22612705X-RAY DIFFRACTION99
2.6215-2.88530.28771500.22052730X-RAY DIFFRACTION99
2.8853-3.30270.25531390.20132733X-RAY DIFFRACTION99
3.3027-4.16050.21441240.16312790X-RAY DIFFRACTION99
4.1605-44.7670.18611670.16232888X-RAY DIFFRACTION99

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