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- PDB-6pvf: Crystal structure of PhqK in complex with malbrancheamide B -

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Basic information

Entry
Database: PDB / ID: 6pvf
TitleCrystal structure of PhqK in complex with malbrancheamide B
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-MB5 / FAD-dependent monooxygenase phqK
Similarity search - Component
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 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 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)52,5473
Polymers51,3921
Non-polymers1,1552
Water8,575476
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)47.950, 82.359, 119.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein FAD monooxygenase


Mass: 51391.941 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 (E. coli) / 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-MB5 / (5aS,12aS,13aS)-9-chloro-12,12-dimethyl-2,3,11,12,12a,13-hexahydro-1H,5H,6H-5a,13a-(epiminomethano)indolizino[7,6-b]carbazol-14-one / malbrancheamide B


Mass: 369.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24ClN3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.04 %
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: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→48.314 Å / Num. obs: 100693 / % possible obs: 99 % / Redundancy: 12 % / Biso Wilson estimate: 25.46 Å2 / CC1/2: 0.72 / Rmerge(I) obs: 0.082 / Net I/σ(I): 1.55
Reflection shellResolution: 1.69→1.75 Å / Num. unique obs: 4655 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
AutoSolphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.69→48.31 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.2069 3778 3.75 %
Rwork0.1702 --
obs0.1716 100627 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.78 Å2 / Biso mean: 30.6982 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 1.69→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 79 476 4055
Biso mean--24.39 40.15 -
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 (%)
1.6901-1.71150.37391160.3532292579
1.7115-1.7340.36371230.3508322889
1.734-1.75770.33421290.324338693
1.7577-1.78290.36091390.3094357298
1.7829-1.80950.311450.29173604100
1.8095-1.83770.35251450.27263692100
1.8377-1.86790.29891400.26753605100
1.8679-1.90010.29881400.25253620100
1.9001-1.93460.31311430.29033663100
1.9346-1.97180.23511390.20213633100
1.9718-2.01210.23941470.18623665100
2.0121-2.05580.24451340.18943593100
2.0558-2.10370.24081380.19453681100
2.1037-2.15630.21981420.18593652100
2.1563-2.21460.2151430.17243662100
2.2146-2.27970.24021370.19383632100
2.2797-2.35330.21681410.16413612100
2.3533-2.43740.19371460.16633654100
2.4374-2.5350.24921420.16983631100
2.535-2.65040.2621440.16513668100
2.6504-2.79010.20811390.16463654100
2.7901-2.96490.16661460.16083630100
2.9649-3.19380.19571420.15473652100
3.1938-3.51510.20381430.1443612100
3.5151-4.02350.15641470.12683658100
4.0235-5.06830.12331440.12753623100
5.0683-48.310.18441440.15153642100
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)
11.23580.1178-0.17821.0831-0.63632.5050.0008-0.04020.07240.1001-0.0402-0.0684-0.14170.1930.04220.1851-0.0077-0.01460.1688-0.01550.180817.737325.81324.2611
20.50220.199-0.16031.0638-0.911.15410.0209-0.0379-0.02040.1037-0.1084-0.0584-0.07140.07840.12210.14090.0144-0.00890.1616-0.02610.168113.898218.790327.903
31.06950.869-0.85141.0203-1.50492.6948-0.15060.0961-0.1805-0.46070.0049-0.11020.425-0.11980.14560.2575-0.01120.00240.2176-0.03080.201310.747615.83698.7601
40.91460.5276-0.62230.6925-0.89511.40610.0044-0.0303-0.02540.05080.03590.0831-0.0397-0.1476-0.0350.19340.01180.00120.179-0.00330.23322.31338.779934.8133
52.50760.53490.0492.40340.14231.71820.042-0.0715-0.10080.1154-0.08630.0220.142-0.03910.03440.15560.0188-0.00420.15690.00160.140522.613812.919717.6705
64.14824.5754-2.63574.9767-2.89681.6512-0.00890.0645-0.2635-0.1189-0.0577-0.0498-0.0019-0.04450.08360.23080.0266-0.01170.24410.00410.29817.3794-1.511635.2203
72.1718-0.0689-1.31521.6693-1.43363.1496-0.16430.0864-0.4049-0.3023-0.0712-0.21410.730.25960.19950.2920.04660.00870.18870.01450.254933.9337.788815.986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 75 )A5 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 150 )A76 - 150
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 188 )A151 - 188
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 310 )A189 - 310
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 378 )A311 - 378
6X-RAY DIFFRACTION6chain 'A' and (resid 379 through 409 )A379 - 409
7X-RAY DIFFRACTION7chain 'A' and (resid 410 through 449 )A410 - 449

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