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- PDB-7ouc: Crystal structure of the flavoprotein monooxygenase GrhO5 from gr... -

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Basic information

Entry
Database: PDB / ID: 7ouc
TitleCrystal structure of the flavoprotein monooxygenase GrhO5 from griseorhodin A biosynthesis
ComponentsPutative FAD-dependent monooxygenase GrhO5
KeywordsFLAVOPROTEIN / monooxygenase / griseorhodin A biosynthesis / rubromycin biosynthesis
Function / homologyAromatic-ring hydroxylase, C-terminal / : / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Putative FAD-dependent monooxygenase GrhO5
Function and homology information
Biological speciesStreptomyces sp. JP95 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: Putative FAD-dependent monooxygenase GrhO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5122
Polymers55,7261
Non-polymers7861
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-7 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.069, 104.437, 69.226
Angle α, β, γ (deg.)90.000, 104.886, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative FAD-dependent monooxygenase GrhO5


Mass: 55726.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. JP95 (bacteria) / Gene: grhO5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KSX7
#2: Chemical ChemComp-FAD / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20 % PEG 3350, 200 mM di-Sodium malonate

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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: Sep 11, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→44.563 Å / Num. obs: 62285 / % possible obs: 97.8 % / Redundancy: 3.2 % / CC1/2: 0.98 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.09 / Net I/σ(I): 5
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 8665 / CC1/2: 0.76

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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: 1.75→44.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.236 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2327 3117 5.03 %
Rwork0.1943 58847 -
all0.196 --
obs-61964 97.23 %
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: 23.034 Å2
Baniso -1Baniso -2Baniso -3
1-0.029 Å2-0 Å20.002 Å2
2---0.042 Å2-0 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 53 475 4413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173774
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.645473
X-RAY DIFFRACTIONr_angle_other_deg1.4451.5778632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.14219.541218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00915580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9051546
X-RAY DIFFRACTIONr_chiral_restr0.0780.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
X-RAY DIFFRACTIONr_nbd_refined0.2020.2831
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23729
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22003
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21936
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2374
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0840.27
X-RAY DIFFRACTIONr_nbd_other0.1570.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.222
X-RAY DIFFRACTIONr_mcbond_it1.9652.2112106
X-RAY DIFFRACTIONr_mcbond_other1.9582.2112105
X-RAY DIFFRACTIONr_mcangle_it2.9163.312629
X-RAY DIFFRACTIONr_mcangle_other2.9153.3112630
X-RAY DIFFRACTIONr_scbond_it2.8262.5391909
X-RAY DIFFRACTIONr_scbond_other2.8282.5411906
X-RAY DIFFRACTIONr_scangle_it4.4123.672844
X-RAY DIFFRACTIONr_scangle_other4.4113.672845
X-RAY DIFFRACTIONr_lrange_it6.03627.2824615
X-RAY DIFFRACTIONr_lrange_other5.84526.6714500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.3241950.323794X-RAY DIFFRACTION84.7641
1.795-1.8450.3072400.294310X-RAY DIFFRACTION98.1873
1.845-1.8980.2972310.2754122X-RAY DIFFRACTION98.5957
1.898-1.9560.2952370.2414040X-RAY DIFFRACTION99.1423
1.956-2.020.2522220.2273949X-RAY DIFFRACTION99.0031
2.02-2.0910.2472010.2043813X-RAY DIFFRACTION98.8427
2.091-2.170.2371860.1923632X-RAY DIFFRACTION98.5799
2.17-2.2590.2132000.1843429X-RAY DIFFRACTION96.2599
2.259-2.3590.21840.1823402X-RAY DIFFRACTION98.5436
2.359-2.4740.2431680.1773259X-RAY DIFFRACTION99.4775
2.474-2.6080.2211770.1843078X-RAY DIFFRACTION99.2378
2.608-2.7660.2561470.1932938X-RAY DIFFRACTION99.1961
2.766-2.9560.2441280.1962745X-RAY DIFFRACTION98.1551
2.956-3.1930.2451250.1912531X-RAY DIFFRACTION96.8283
3.193-3.4960.2231060.1772317X-RAY DIFFRACTION96.5339
3.496-3.9080.165990.1552143X-RAY DIFFRACTION98.5061
3.908-4.510.186840.1561882X-RAY DIFFRACTION97.3749
4.51-5.5170.223840.1791557X-RAY DIFFRACTION96.5862
5.517-7.7760.26560.2041217X-RAY DIFFRACTION94.7173
7.776-44.520.214470.198689X-RAY DIFFRACTION98.0027

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