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- PDB-6pvg: Crystal structure of ligand free PhqK -

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Basic information

Entry
Database: PDB / ID: 6pvg
TitleCrystal structure of ligand free PhqK
ComponentsFAD monooxygenase
KeywordsBIOSYNTHETIC PROTEIN / monooxygenase / flavin
Function / homologyFAD-binding domain / FAD binding domain / Oxidoreductases / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / FAD-dependent monooxygenase phqK
Function and homology information
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.709 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)52,1312
Polymers51,3451
Non-polymers7861
Water7,206400
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)47.724, 84.210, 116.389
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
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: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.7→47.88 Å / Num. obs: 630819 / % possible obs: 99 % / Redundancy: 12.4 % / Net I/σ(I): 1.34
Reflection shellResolution: 1.71→1.77 Å / Num. unique obs: 4603

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Processing

SoftwareName: PHENIX / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.709→47.875 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.71
RfactorNum. reflection% reflection
Rfree0.192 3820 3.96 %
Rwork0.1623 --
obs0.1635 96541 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.01 Å2 / Biso mean: 37.5218 Å2 / Biso min: 18.29 Å2
Refinement stepCycle: final / Resolution: 1.709→47.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 53 400 3961
Biso mean--25.59 46.33 -
Num. residues----445
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7095-1.73110.42461120.4063282382
1.7311-1.75390.33361370.3348325993
1.7539-1.77790.3231330.2974334996
1.7779-1.80330.31321360.2653332496
1.8033-1.83020.27681380.2374346797
1.8302-1.85880.25741430.2228342199
1.8588-1.88930.23641430.2077344799
1.8893-1.92190.25651430.2049347299
1.9219-1.95680.2261390.20823449100
1.9568-1.99450.23191470.20483519100
1.9945-2.03520.21291450.17443433100
2.0352-2.07940.22341430.1723530100
2.0794-2.12780.18771440.16823440100
2.1278-2.1810.17951430.16853491100
2.181-2.240.24991440.17113484100
2.24-2.30590.21551450.17283496100
2.3059-2.38030.24831360.17123483100
2.3803-2.46540.27821410.17313477100
2.4654-2.56410.21881450.18083476100
2.5641-2.68080.23321500.17863482100
2.6808-2.82210.24011440.17933492100
2.8221-2.99890.16411400.16593508100
2.9989-3.23040.1931470.16393468100
3.2304-3.55540.15551440.14533480100
3.5554-4.06970.15271390.1313498100
4.0697-5.12640.13771500.11813479100
5.1264-47.8750.14421490.13443474100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.508-0.7070.47482.49381.22893.2966-0.04690.24330.5588-0.2130.1408-0.2729-0.41830.2072-0.11180.2431-0.03730.02210.22140.00980.262820.075329.723715.5092
20.56580.0284-0.1861.1798-0.96461.13720.0256-0.03050.00890.1537-0.0966-0.0542-0.08660.09170.10240.2099-0.0077-0.00580.222-0.02340.210814.987719.913229.1433
31.27120.9498-0.86611.8128-1.60232.3145-00.139-0.1569-0.3791-0.1935-0.08760.3491-0.07730.18980.28380.00440.01180.2924-0.05490.205511.742817.26258.0472
41.08260.4751-0.56670.8641-0.96521.09580.0396-0.03840.00550.06250.06850.119-0.0893-0.1435-0.11320.24960.01240.02580.216-0.00460.25272.46917.549334.2932
54.2054-0.22540.58921.29151.22023.2127-0.0837-0.1050.05720.0078-0.0151-0.0373-0.01270.02850.08450.17460.029-0.00780.17230.01570.184923.930118.181817.3856
61.60772.3551-1.5692.2577-2.21291.483-0.0555-0.0635-0.1588-0.0884-0.0587-0.11250.15460.0610.11920.2830.05060.06590.2780.02330.327120.50052.741126.2307
72.1983-0.5794-0.98691.5197-2.23515.3088-0.2645-0.0206-0.5556-0.385-0.06560.01040.93260.46170.29590.30870.05680.05290.2420.04590.319435.12158.805616.4243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 37 )A4 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 149 )A38 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 187 )A150 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 309 )A188 - 309
5X-RAY DIFFRACTION5chain 'A' and (resid 310 through 350 )A310 - 350
6X-RAY DIFFRACTION6chain 'A' and (resid 351 through 408 )A351 - 408
7X-RAY DIFFRACTION7chain 'A' and (resid 409 through 448 )A409 - 448

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