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- PDB-7ouj: Crystal structure of the flavoprotein monooxygenase RubL from rub... -

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Basic information

Entry
Database: PDB / ID: 7ouj
TitleCrystal structure of the flavoprotein monooxygenase RubL from rubromycin biosynthesis
ComponentsRubL
KeywordsFLAVOPROTEIN / monooxygenase / griseorhodin A biosynthesis / rubromycin biosynthesis
Function / homologyFAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / (2S)-hexane-1,2,6-triol / FLAVIN-ADENINE DINUCLEOTIDE / 4-HYDROXYPROLINE / Putative polyketide hydroxylase
Function and homology information
Biological speciesStreptomyces collinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.573 Å
AuthorsSaleem-Batcha, R. / Toplak, M. / Teufel, R.
Funding support Germany, Austria, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)TE 931/3-1 Germany
German Research Foundation (DFG)TE 931/4-1 Germany
Austrian Science FundJ4482-B Austria
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Catalytic Control of Spiroketal Formation in Rubromycin Polyketide Biosynthesis.
Authors: Toplak, M. / Saleem-Batcha, R. / Piel, J. / Teufel, R.
History
DepositionJun 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: RubL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3658
Polymers57,9191
Non-polymers1,4477
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-19 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.323, 57.514, 122.379
Angle α, β, γ (deg.)90.000, 95.183, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein RubL


Mass: 57918.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HYP is ligand from crystallisation buffer / Source: (gene. exp.) Streptomyces collinus (bacteria) / Gene: rubL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KY42

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Non-polymers , 6 types, 201 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1JW / (2S)-hexane-1,2,6-triol / (-)-1,2,6-Hexanetriol / 6999990


Mass: 134.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O3
#5: Chemical ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE / Hydroxyproline


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 47.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA ...Details: 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA pH 7.5 buffer system, 12.5% PEG 4000 and 20% 1,2,6-Hexanetriol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→46.08 Å / Num. obs: 70014 / % possible obs: 94 % / Redundancy: 2.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.4
Reflection shellResolution: 1.57→1.66 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 10481 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IHG

3ihg


Resolution: 1.573→37.778 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.18 / SU B: 2.014 / SU ML: 0.066 / Average fsc free: 0.8812 / Average fsc work: 0.8859 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2095 3673 5.247 %
Rwork0.183 66335 -
all0.184 --
obs-70008 94.034 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å20 Å2-0.002 Å2
2--0.051 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.573→37.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 96 194 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134145
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173915
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.655651
X-RAY DIFFRACTIONr_angle_other_deg1.5111.5878984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75819.539217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7315596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0241547
X-RAY DIFFRACTIONr_chiral_restr0.0850.2530
X-RAY DIFFRACTIONr_chiral_restr_other0.0530.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02931
X-RAY DIFFRACTIONr_nbd_refined0.210.2777
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23778
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22060
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2204
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2910.26
X-RAY DIFFRACTIONr_nbd_other0.2250.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.27
X-RAY DIFFRACTIONr_mcbond_it2.2752.6812162
X-RAY DIFFRACTIONr_mcbond_other2.2752.6812162
X-RAY DIFFRACTIONr_mcangle_it3.1844.0162699
X-RAY DIFFRACTIONr_mcangle_other3.1834.0182700
X-RAY DIFFRACTIONr_scbond_it3.5243.051983
X-RAY DIFFRACTIONr_scbond_other3.5233.051984
X-RAY DIFFRACTIONr_scangle_it5.2254.4112952
X-RAY DIFFRACTIONr_scangle_other5.2254.4112953
X-RAY DIFFRACTIONr_lrange_it6.22531.7574435
X-RAY DIFFRACTIONr_lrange_other6.20131.6634415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.573-1.6140.3762500.3735023X-RAY DIFFRACTION95.4389
1.614-1.6580.3342650.3344936X-RAY DIFFRACTION98.0951
1.658-1.7060.2932610.294795X-RAY DIFFRACTION97.3806
1.706-1.7590.2622650.2584653X-RAY DIFFRACTION97.444
1.759-1.8160.262540.2314411X-RAY DIFFRACTION96.1261
1.816-1.880.2392390.2074135X-RAY DIFFRACTION91.7943
1.88-1.9510.1952320.1724127X-RAY DIFFRACTION96.2889
1.951-2.030.2062120.1564044X-RAY DIFFRACTION96.1156
2.03-2.1210.181940.1523829X-RAY DIFFRACTION95.1289
2.121-2.2240.2051930.1523617X-RAY DIFFRACTION94.5879
2.224-2.3440.1912180.1623409X-RAY DIFFRACTION94.2078
2.344-2.4860.2051880.1693190X-RAY DIFFRACTION93.4181
2.486-2.6580.1811530.1692948X-RAY DIFFRACTION89.8841
2.658-2.870.2141730.1612777X-RAY DIFFRACTION92.3896
2.87-3.1430.1871480.1582543X-RAY DIFFRACTION91.9686
3.143-3.5140.1811300.1572262X-RAY DIFFRACTION89.5545
3.514-4.0550.1921140.1711961X-RAY DIFFRACTION87.775
4.055-4.9620.21720.1741628X-RAY DIFFRACTION84.4091
4.962-6.9990.213760.2111289X-RAY DIFFRACTION87.1648
6.999-37.7780.184360.163758X-RAY DIFFRACTION87.9291

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