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- PDB-7oud: Crystal structure of a ternary complex of the flavoprotein monoox... -

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Basic information

Entry
Database: PDB / ID: 7oud
TitleCrystal structure of a ternary complex of the flavoprotein monooxygenase GrhO5 with FAD and collinone
ComponentsFAD-dependent monooxygenase GrhO5
KeywordsFLAVOPROTEIN / monooxygenase / griseorhodin A biosynthesis / rubromycin biosynthesis
Function / homology
Function and homology information


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
Similarity search - Function
Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Collinone / FLAVIN-ADENINE DINUCLEOTIDE / Putative FAD-dependent monooxygenase GrhO5
Similarity search - Component
Biological speciesStreptomyces sp. JP95 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2May 1, 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

Downloads & links

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Assembly

Deposited unit
AAA: FAD-dependent monooxygenase GrhO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4393
Polymers56,1191
Non-polymers1,3202
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.666, 103.747, 69.005
Angle α, β, γ (deg.)90.000, 104.594, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FAD-dependent monooxygenase GrhO5 / Flavoprotein monooxygenase GrhO5


Mass: 56118.578 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: Chemical ChemComp-1J0 / Collinone / 135469160


Mass: 534.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H18O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20 % PEG 3350, 200mM 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: 2.3→44.19 Å / Num. obs: 26914 / % possible obs: 97 % / Redundancy: 3.2 % / CC1/2: 0.92 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.49 / Num. unique obs: 3911 / CC1/2: 0.83

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Processing

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

Resolution: 2.3→44.19 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.832 / SU B: 9.027 / SU ML: 0.209 / Cross valid method: NONE / ESU R: 0.377 / ESU R Free: 0.254
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2629 1392 5.178 %
Rwork0.225 25490 -
all0.227 --
obs-26882 97.156 %
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: 9.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.043 Å20 Å2-0.002 Å2
2--0.015 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 92 278 4255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134059
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173787
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.655546
X-RAY DIFFRACTIONr_angle_other_deg1.2951.588660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4735525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35819.541218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78515580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261546
X-RAY DIFFRACTIONr_chiral_restr0.0710.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02936
X-RAY DIFFRACTIONr_nbd_refined0.1980.2909
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.23877
X-RAY DIFFRACTIONr_nbtor_refined0.160.21973
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.220
X-RAY DIFFRACTIONr_nbd_other0.2090.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.219
X-RAY DIFFRACTIONr_mcbond_it0.9130.9542106
X-RAY DIFFRACTIONr_mcbond_other0.9130.9542105
X-RAY DIFFRACTIONr_mcangle_it1.6461.4252629
X-RAY DIFFRACTIONr_mcangle_other1.6461.4252630
X-RAY DIFFRACTIONr_scbond_it0.8931.0531953
X-RAY DIFFRACTIONr_scbond_other0.8921.0541954
X-RAY DIFFRACTIONr_scangle_it1.5971.5392917
X-RAY DIFFRACTIONr_scangle_other1.5971.542918
X-RAY DIFFRACTIONr_lrange_it3.42110.6514679
X-RAY DIFFRACTIONr_lrange_other3.34810.6564627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.351150.2931851X-RAY DIFFRACTION97.2305
2.36-2.4240.3181080.2851823X-RAY DIFFRACTION97.3286
2.424-2.4940.358790.2771808X-RAY DIFFRACTION97.5194
2.494-2.5710.28910.281753X-RAY DIFFRACTION97.8769
2.571-2.6550.364870.251679X-RAY DIFFRACTION97.623
2.655-2.7480.262810.241615X-RAY DIFFRACTION97.4153
2.748-2.8520.306770.2351592X-RAY DIFFRACTION97.3746
2.852-2.9680.274950.2391510X-RAY DIFFRACTION98.5267
2.968-3.10.272750.231446X-RAY DIFFRACTION97.2506
3.1-3.2510.283860.2191305X-RAY DIFFRACTION91.3329
3.251-3.4260.241640.2111311X-RAY DIFFRACTION96.2211
3.426-3.6330.233720.1941265X-RAY DIFFRACTION98.5988
3.633-3.8830.181640.1811175X-RAY DIFFRACTION98.4897
3.883-4.1930.199690.1781112X-RAY DIFFRACTION98.4987
4.193-4.5920.191670.1651014X-RAY DIFFRACTION98.3621
4.592-5.1310.251470.169921X-RAY DIFFRACTION97.5807
5.131-5.9190.223410.216788X-RAY DIFFRACTION96.2834
5.919-7.2350.226240.207661X-RAY DIFFRACTION91.7001
7.235-10.1720.188320.172546X-RAY DIFFRACTION99.4837
10.172-44.190.319180.306315X-RAY DIFFRACTION97.654

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