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- PDB-7vwp: Structure of the flavin-dependent monooxygenase FlsO1 from the bi... -

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Basic information

Entry
Database: PDB / ID: 7vwp
TitleStructure of the flavin-dependent monooxygenase FlsO1 from the biosynthesis of fluostatinsin
ComponentsFlsO1
KeywordsOXIDOREDUCTASE / hydroxylation / benzo[b]-fluorene / epoxidation / Baeyer-Villiger Oxidation / prejadomycin
Function / homologyFAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / FlsO1
Function and homology information
Biological speciesMicromonospora rosaria (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, Y. / Yang, C. / Zhang, L. / Zhang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31820103003 China
CitationJournal: Nat Commun / Year: 2022
Title: Biochemical and structural insights of multifunctional flavin-dependent monooxygenase FlsO1-catalyzed unexpected xanthone formation
Authors: Yang, C. / Zhang, L. / Zhang, W. / Huang, C. / Zhu, Y. / Jiang, X. / Liu, W. / Zhao, M. / De, B.C. / Zhang, C.
History
DepositionNov 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: FlsO1
A: FlsO1
B: FlsO1
C: FlsO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,60323
Polymers213,1084
Non-polymers4,49519
Water18,2851015
1
A: FlsO1
hetero molecules

D: FlsO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69510
Polymers106,5542
Non-polymers2,1418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area6220 Å2
ΔGint-74 kcal/mol
Surface area37170 Å2
MethodPISA
2
B: FlsO1
hetero molecules

C: FlsO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,90813
Polymers106,5542
Non-polymers2,35411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area6670 Å2
ΔGint-97 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.540, 84.636, 102.799
Angle α, β, γ (deg.)91.314, 107.860, 115.391
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FlsO1


Mass: 53276.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora rosaria (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0P0I576
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1015 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, pH 6.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.3→13.182 Å / Num. obs: 95967 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4703

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.2-4158refinement
Aimlessdata scaling
MOLREPphasing
CrysalisPro1.171.39.7edata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QA1

2qa1


Resolution: 2.3→13.182 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.819 / SU ML: 0.207 / Cross valid method: FREE R-VALUE / ESU R: 0.374 / ESU R Free: 0.265
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2709 4704 4.922 %
Rwork0.2115 90862 -
all0.214 --
obs-95566 98.523 %
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: 29.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.811 Å2-1.894 Å20.969 Å2
2---0.351 Å20.291 Å2
3---0.332 Å2
Refinement stepCycle: LAST / Resolution: 2.3→13.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14414 0 283 1015 15712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01315032
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714106
X-RAY DIFFRACTIONr_angle_refined_deg1.51.64120454
X-RAY DIFFRACTIONr_angle_other_deg1.2931.57832248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11151912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76720.113798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.835152237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.54115152
X-RAY DIFFRACTIONr_chiral_restr0.0660.21882
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023520
X-RAY DIFFRACTIONr_nbd_refined0.2070.23135
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.213931
X-RAY DIFFRACTIONr_nbtor_refined0.1630.27048
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.27918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.21038
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.110.219
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.234
X-RAY DIFFRACTIONr_nbd_other0.2670.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.290.27
X-RAY DIFFRACTIONr_mcbond_it2.2273.0637699
X-RAY DIFFRACTIONr_mcbond_other2.2273.0637698
X-RAY DIFFRACTIONr_mcangle_it3.5064.5779594
X-RAY DIFFRACTIONr_mcangle_other3.5064.5779595
X-RAY DIFFRACTIONr_scbond_it2.2713.227333
X-RAY DIFFRACTIONr_scbond_other2.2673.227330
X-RAY DIFFRACTIONr_scangle_it3.5834.76310860
X-RAY DIFFRACTIONr_scangle_other3.5834.76310861
X-RAY DIFFRACTIONr_lrange_it6.01535.21516815
X-RAY DIFFRACTIONr_lrange_other5.95435.11416583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3693550.2766690X-RAY DIFFRACTION97.5897
2.36-2.4240.3073260.2556541X-RAY DIFFRACTION98.8769
2.424-2.4950.3253220.2446472X-RAY DIFFRACTION99.6626
2.495-2.5710.3423250.2516309X-RAY DIFFRACTION99.6994
2.571-2.6560.3353150.2496020X-RAY DIFFRACTION99.8896
2.656-2.7490.3193170.2465879X-RAY DIFFRACTION99.6142
2.749-2.8520.2922600.2325671X-RAY DIFFRACTION99.5301
2.852-2.9690.2942670.2345459X-RAY DIFFRACTION99.4788
2.969-3.1010.312570.2325200X-RAY DIFFRACTION99.2182
3.101-3.2520.2972660.2284964X-RAY DIFFRACTION99.1469
3.252-3.4270.2862460.2264714X-RAY DIFFRACTION99.2397
3.427-3.6350.2482320.2124470X-RAY DIFFRACTION98.5125
3.635-3.8860.2762630.1994117X-RAY DIFFRACTION99.1174
3.886-4.1960.2422070.1853867X-RAY DIFFRACTION98.501
4.196-4.5960.1981920.1543573X-RAY DIFFRACTION98.793
4.596-5.1370.2041630.1553269X-RAY DIFFRACTION98.6774
5.137-5.9290.2171510.1872853X-RAY DIFFRACTION99.0112
5.929-7.2550.211210.1962422X-RAY DIFFRACTION98.9879
7.255-10.2310.188880.1531871X-RAY DIFFRACTION98.3928
10.231-13.1820.236310.183501X-RAY DIFFRACTION48.2321

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