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- PDB-6pvh: Crystal structure of PhqK in complex with paraherquamide K -

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Basic information

Entry
Database: PDB / ID: 6pvh
TitleCrystal structure of PhqK in complex with paraherquamide K
ComponentsFAD monooxygenase
KeywordsBIOSYNTHETIC PROTEIN / monooxygenase / 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-OZ4 / FAD-dependent monooxygenase phqK
Similarity search - Component
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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)52,5623
Polymers51,3451
Non-polymers1,2172
Water3,981221
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)48.164, 83.237, 119.615
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-OZ4 / (7aS,12S,12aR,13aS)-3,3,12,14,14-pentamethyl-3,7,11,12,13,13a,14,15-octahydro-8H,10H-7a,12a-(epiminomethano)indolizino[6,7-h]pyrano[3,2-a]carbazol-16-one


Mass: 431.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 47.32 %
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, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.89→44.68 Å / Num. obs: 495499 / % possible obs: 99 % / Redundancy: 12.7 % / CC1/2: 0.56 / Net I/σ(I): 1.14
Reflection shellResolution: 1.89→1.96 Å / Rmerge(I) obs: 1.463 / Num. unique obs: 3831

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→44.678 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 3690 4.97 %
Rwork0.2151 70623 -
obs0.217 74313 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.32 Å2 / Biso mean: 38.865 Å2 / Biso min: 14.43 Å2
Refinement stepCycle: final / Resolution: 1.89→44.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 85 221 3806
Biso mean--39.37 39.64 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.89-1.91490.44431470.48232726
1.9149-1.94110.45091430.41782731
1.9411-1.96890.32721420.34642717
1.9689-1.99820.36341400.31972698
1.9982-2.02950.37781440.312689
2.0295-2.06270.35821340.29292693
2.0627-2.09830.36521480.3052790
2.0983-2.13650.36761390.29292676
2.1365-2.17760.36171410.31282716
2.1776-2.2220.36351430.31272712
2.222-2.27030.46471430.32762686
2.2703-2.32310.30281390.32162730
2.3231-2.38120.35691450.31382725
2.3812-2.44560.371420.31532732
2.4456-2.51760.33411450.29582697
2.5176-2.59880.37931400.29292752
2.5988-2.69170.27131470.27142705
2.6917-2.79940.3271380.25052694
2.7994-2.92680.2541430.22062718
2.9268-3.08110.23451390.20252724
3.0811-3.27410.21531430.17412696
3.2741-3.52680.2391370.16462718
3.5268-3.88150.17891390.14612730
3.8815-4.44270.16121420.12892735
4.4427-5.59570.15781400.12892708
5.5957-44.6780.16211470.15282725
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)
12.145-0.49980.7312.4611.15874.870.07650.01470.0672-0.0921-0.05320.076-0.1972-0.22270.0120.2005-0.02190.00510.15950.02240.197630.327967.62736.7753
20.5381-0.0755-0.14811.49461.39112.3364-0.0159-0.0189-0.02990.0996-0.05970.09140.09-0.04530.07130.1674-0.02140.01470.22350.01720.250535.126160.084537.4682
31.0253-0.48-0.34432.65810.172.38810.06010.0280.0763-0.05550.0147-0.2488-0.29470.1773-0.07490.2474-0.00020.00050.2665-0.03110.300247.732849.678222.2572
42.5321-1.2423-0.89165.23421.58544.0964-0.02060.029-0.1359-0.0135-0.0438-0.08240.10170.09510.04510.1548-0.04040.00960.16370.01360.180224.84355.715544.4878
56.1239-6.2603-4.41396.13234.56953.6368-0.1401-0.4375-0.00340.22030.1829-0.16990.10480.31080.01940.2966-0.0641-0.01720.33310.00540.418531.660639.279625.4177
63.3612-0.0204-1.92623.25852.87293.6982-0.3617-0.1379-0.52160.5020.0430.35460.9895-0.18420.26320.4209-0.04240.03840.25040.01290.313214.353349.371743.5641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 70 )A5 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 187 )A71 - 187
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 299 )A188 - 299
4X-RAY DIFFRACTION4chain 'A' and (resid 300 through 374 )A300 - 374
5X-RAY DIFFRACTION5chain 'A' and (resid 375 through 408 )A375 - 408
6X-RAY DIFFRACTION6chain 'A' and (resid 409 through 448 )A409 - 448

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