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- PDB-8r20: X-ray crystallographic structure of KstA15, polyketide biosynthes... -

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Basic information

Entry
Database: PDB / ID: 8r20
TitleX-ray crystallographic structure of KstA15, polyketide biosynthesis enzyme
ComponentsHydroxylase
KeywordsBIOSYNTHETIC PROTEIN / Polyketide / antibiotic / biosynthesis
Function / homologypolyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / NTF2-like domain superfamily / Hydroxylase
Function and homology information
Biological speciesMicromonospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03999 Sweden
CitationJournal: Acs Catalysis / Year: 2024
Title: Mechanism of Two-Component Mono-Oxygenases Involved in Anthracycline 1-Hydroxylation
Authors: Wandi, B.N. / Dinis, P. / Siitonen, V. / Schneider, G. / Schnell, R. / Metsa-Ketele, M.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxylase
B: Hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1523
Polymers35,0602
Non-polymers921
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, identical mode of deimrization as seen in the cases of several homologues
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area13680 Å2
Unit cell
Length a, b, c (Å)48.975, 52.751, 108.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydroxylase


Mass: 17530.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora (bacteria) / Plasmid: pNIC28Bsa4
Details (production host): N-terminal His6-tag, Removable by TEV-protease cleavage
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023GUN4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 34 % / Description: short rod
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.75
Details: 0.1 M Bis-TRIS-Propane pH 7.75, 2.2 M ammonium-sulfate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2018 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.1→44.61 Å / Num. obs: 17018 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 56.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.063 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2 / Num. unique obs: 1365 / CC1/2: 0.732 / Rpim(I) all: 0.532 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.61 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.528 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23091 821 4.8 %RANDOM
Rwork0.18487 ---
obs0.18707 16150 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 6 109 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132329
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172204
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6383155
X-RAY DIFFRACTIONr_angle_other_deg1.2861.5885086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10721.765136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36515420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5471520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6023.341110
X-RAY DIFFRACTIONr_mcbond_other2.5983.3391109
X-RAY DIFFRACTIONr_mcangle_it3.7464.9891384
X-RAY DIFFRACTIONr_mcangle_other3.7444.9911385
X-RAY DIFFRACTIONr_scbond_it3.7783.8431219
X-RAY DIFFRACTIONr_scbond_other3.7773.8431220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8855.5821772
X-RAY DIFFRACTIONr_long_range_B_refined7.26839.5942571
X-RAY DIFFRACTIONr_long_range_B_other7.26739.5982572
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 55 -
Rwork0.254 1175 -
obs--100 %

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