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- PDB-6pvj: Crystal structure of PhqK in complex with malbrancheamide C -

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Basic information

Entry
Database: PDB / ID: 6pvj
TitleCrystal structure of PhqK in complex with malbrancheamide C
ComponentsFAD monooxygenase
KeywordsBIOSYNTHETIC PROTEIN / flavin
Function / homology
Function and homology information


Oxidoreductases / FAD binding / monooxygenase activity
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-OZA / FAD-dependent monooxygenase phqK
Similarity search - Component
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsFraley, A.E. / Smith, J.L. / Sherman, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 CA70375 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway.
Authors: Fraley, A.E. / Caddell Haatveit, K. / Ye, Y. / Kelly, S.P. / Newmister, S.A. / Yu, F. / Williams, R.M. / Smith, J.L. / Houk, K.N. / Sherman, D.H.
History
DepositionJul 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5453
Polymers51,3451
Non-polymers1,2002
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.077, 82.801, 120.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FAD monooxygenase


Mass: 51345.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium fellutanum (fungus) / Gene: phqK / Plasmid: pKLD116 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L0E4H0
#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-OZA / (5aS,12aS,13aS)-9-bromo-12,12-dimethyl-2,3,11,12,12a,13-hexahydro-1H,5H,6H-5a,13a-(epiminomethano)indolizino[7,6-b]carbazol-14-one


Mass: 414.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24BrN3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 200 mM ammonium acetate, 100 mM Bis-Tris pH 5.5, 2% 2,2,2-trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.7293 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.25→31.372 Å / Num. obs: 1725902 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 1.11
Reflection shellResolution: 1.25→1.3 Å / Num. unique obs: 13092 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→31.372 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1751 3857 1.51 %
Rwork0.1542 252033 -
obs0.1545 255890 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.35 Å2 / Biso mean: 26.0925 Å2 / Biso min: 11.59 Å2
Refinement stepCycle: final / Resolution: 1.25→31.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 79 616 4195
Biso mean--19.8 40.5 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.25-1.26520.32281370.3121872596
1.2652-1.28130.30921390.3022895299
1.2813-1.29810.29121410.27529038100
1.2981-1.31590.30621370.26638948100
1.3159-1.33470.27591370.24829071100
1.3347-1.35460.28131380.24128928100
1.3546-1.37580.26131390.23759106100
1.3758-1.39840.25511390.22938983100
1.3984-1.42250.25511390.229033100
1.4225-1.44830.27971390.21178994100
1.4483-1.47620.25061380.19599021100
1.4762-1.50630.26641390.18539015100
1.5063-1.53910.15761350.16349028100
1.5391-1.57490.1921360.15228914100
1.5749-1.61430.16911400.14769095100
1.6143-1.65790.19631380.14789042100
1.6579-1.70670.19061380.14628995100
1.7067-1.76180.18311370.14748999100
1.7618-1.82470.2141350.15228992100
1.8247-1.89780.14991390.14449054100
1.8978-1.98410.15721370.14019001100
1.9841-2.08870.16441410.14129034100
2.0887-2.21960.13711340.13758969100
2.2196-2.39090.13831340.13379067100
2.3909-2.63140.16541400.14988961100
2.6314-3.01190.15411410.14969069100
3.0119-3.79360.15671300.13558979100
3.7936-31.3720.16871400.14259020100

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