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- PDB-8r2b: X-ray crystallographic structure of SnoaL2 in complex with the po... -

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Basic information

Entry
Database: PDB / ID: 8r2b
TitleX-ray crystallographic structure of SnoaL2 in complex with the polyketide substrate
ComponentsSnoL
KeywordsBIOSYNTHETIC PROTEIN / Polyketide / antibiotic / biosynthesis
Function / homologypolyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / NTF2-like domain superfamily / : / SnoL
Function and homology information
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SnoL
B: SnoL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3993
Polymers33,8262
Non-polymers5731
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimerization mode common in the protein family and related proteins
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-5 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.628, 62.281, 89.814
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 SnoL


Mass: 16913.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag (sequence: MAHHHHHHRS) used in purification.
Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: snoL / Plasmid: pBAD
Details (production host): N-termial His6-tag, not removable
Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9RN64
#2: Chemical ChemComp-XN0 / 3',4'-demethoxy-nogalose-nogalamycinone / methyl (1R,2S,4S)-4-[(2R,3R,4R,5S,6S)-3-methoxy-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-methyl-2,5,7-tris(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1H-tetracene-1-carboxylate / methyl 4-(4,5-dihydroxy-3-methoxy-4,6-dimethyloxan-2-yl)oxy-2,5,7-trihydroxy-2-methyl-6,11-dioxo-3,4-dihydro-1H-tetracene-1-carboxylate / methyl (1R,2S,4S)-4-[(2R,3R,4R,5S,6S)-4,5-dihydroxy-3-methoxy-4,6-dimethyloxan-2-yl]oxy-2,5,7-trihydroxy-2-methyl-6,11-dioxo-3,4-dihydro-1H-tetracene-1-carboxylate


Mass: 572.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32O12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.18 Å3/Da / Density % sol: 39.1 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.2 M MgCl2, 25% PEG3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87312 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: 0.87312 Å / Relative weight: 1
ReflectionResolution: 1.8→36.69 Å / Num. obs: 27685 / % possible obs: 98.9 % / Observed criterion σ(I): 1.7 / Redundancy: 4.3 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.046 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1569 / CC1/2: 0.67 / Rpim(I) all: 0.477 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.558 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22969 1368 4.9 %RANDOM
Rwork0.19178 ---
obs0.19368 26280 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.944 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å2-0 Å20 Å2
2---2.18 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.8→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 41 257 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192225
X-RAY DIFFRACTIONr_bond_other_d0.0030.022044
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9413038
X-RAY DIFFRACTIONr_angle_other_deg1.0943.0054677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1755265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98322.743113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75115352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4311524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022515
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02545
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_it2.5652.9781057
X-RAY DIFFRACTIONr_mcbond_other2.5562.9731056
X-RAY DIFFRACTIONr_mcangle_it3.7014.4351323
X-RAY DIFFRACTIONr_mcangle_other3.74.441324
X-RAY DIFFRACTIONr_scbond_it3.7733.3821168
X-RAY DIFFRACTIONr_scbond_other3.7723.3811169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.744.8941716
X-RAY DIFFRACTIONr_long_range_B_refined8.18528.9669774
X-RAY DIFFRACTIONr_long_range_B_other8.09528.6779533
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 90 -
Rwork0.328 1893 -
obs--97.25 %

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