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- PDB-6qlg: Crystal structure of AnUbiX (PadA1) in complex with FMN and dimet... -

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Basic information

Entry
Database: PDB / ID: 6qlg
TitleCrystal structure of AnUbiX (PadA1) in complex with FMN and dimethylallyl pyrophosphate
ComponentsFlavin prenyltransferase PAD1, mitochondrial
KeywordsTRANSFERASE / UbiX Prenyltransferase Flavin binding
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / mitochondrion
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIMETHYLALLYL DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Flavin prenyltransferase PAD1, mitochondrial
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMarshall, S.A. / Payne, K.A.P. / Leys, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K017802/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P000622/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry.
Authors: Marshall, S.A. / Payne, K.A.P. / Fisher, K. / White, M.D. / Ni Cheallaigh, A. / Balaikaite, A. / Rigby, S.E.J. / Leys, D.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 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
C: Flavin prenyltransferase PAD1, mitochondrial
A: Flavin prenyltransferase PAD1, mitochondrial
B: Flavin prenyltransferase PAD1, mitochondrial
D: Flavin prenyltransferase PAD1, mitochondrial
E: Flavin prenyltransferase PAD1, mitochondrial
F: Flavin prenyltransferase PAD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,99621
Polymers150,4746
Non-polymers4,52215
Water10,629590
1
C: Flavin prenyltransferase PAD1, mitochondrial
A: Flavin prenyltransferase PAD1, mitochondrial
B: Flavin prenyltransferase PAD1, mitochondrial
D: Flavin prenyltransferase PAD1, mitochondrial
E: Flavin prenyltransferase PAD1, mitochondrial
F: Flavin prenyltransferase PAD1, mitochondrial
hetero molecules

C: Flavin prenyltransferase PAD1, mitochondrial
A: Flavin prenyltransferase PAD1, mitochondrial
B: Flavin prenyltransferase PAD1, mitochondrial
D: Flavin prenyltransferase PAD1, mitochondrial
E: Flavin prenyltransferase PAD1, mitochondrial
F: Flavin prenyltransferase PAD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,99142
Polymers300,94712
Non-polymers9,04430
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area70770 Å2
ΔGint-415 kcal/mol
Surface area58000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.000, 102.000, 276.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-470-

HOH

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Components

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Protein , 1 types, 6 molecules CABDEF

#1: Protein
Flavin prenyltransferase PAD1, mitochondrial


Mass: 25078.951 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: PAD1, An03g06570 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3F715, flavin prenyltransferase

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Non-polymers , 5 types, 605 molecules

#2: Chemical
ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: JCSG + D3 (Molecular Dimensions): 0.2 M NaCl, 0.1 M Na/K Phosphate pH 6.2, 30% v/v PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→95.7 Å / Num. obs: 80295 / % possible obs: 99.98 % / Redundancy: 14.7 % / Biso Wilson estimate: 29.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1247 / Net I/σ(I): 15.5
Reflection shellResolution: 2.15→2.27 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→95.7 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.881
RfactorNum. reflection% reflection
Rfree0.1825 4016 5 %
Rwork0.1611 --
obs0.1622 80280 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.66 Å2
Refinement stepCycle: LAST / Resolution: 2.15→95.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8733 0 289 590 9612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00259388
X-RAY DIFFRACTIONf_angle_d0.529212797
X-RAY DIFFRACTIONf_chiral_restr0.04161448
X-RAY DIFFRACTIONf_plane_restr0.00291606
X-RAY DIFFRACTIONf_dihedral_angle_d9.38967592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.22361330.1982557X-RAY DIFFRACTION99.85
2.18-2.20.27531530.19762578X-RAY DIFFRACTION100
2.2-2.230.23081260.18742586X-RAY DIFFRACTION100
2.23-2.260.2091580.18152598X-RAY DIFFRACTION100
2.26-2.290.21911460.18362551X-RAY DIFFRACTION100
2.29-2.320.21121410.17682612X-RAY DIFFRACTION99.96
2.32-2.360.2231220.17242582X-RAY DIFFRACTION99.93
2.36-2.390.2381540.182552X-RAY DIFFRACTION99.96
2.39-2.430.20151300.18362617X-RAY DIFFRACTION99.96
2.43-2.480.18711320.16372605X-RAY DIFFRACTION100
2.48-2.520.211170.17532604X-RAY DIFFRACTION100
2.52-2.570.21380.16342599X-RAY DIFFRACTION100
2.57-2.620.20071580.16672616X-RAY DIFFRACTION100
2.62-2.680.2041300.17052605X-RAY DIFFRACTION100
2.68-2.740.19311370.17242583X-RAY DIFFRACTION100
2.74-2.810.19661350.16862618X-RAY DIFFRACTION100
2.81-2.890.19381270.16832639X-RAY DIFFRACTION100
2.89-2.970.20051250.1732617X-RAY DIFFRACTION100
2.97-3.070.19341480.16992620X-RAY DIFFRACTION100
3.07-3.180.2051390.17442627X-RAY DIFFRACTION100
3.18-3.30.1791420.16522631X-RAY DIFFRACTION100
3.3-3.450.18681330.16192634X-RAY DIFFRACTION99.96
3.45-3.640.20021340.16442661X-RAY DIFFRACTION100
3.64-3.860.1451410.14352639X-RAY DIFFRACTION100
3.86-4.160.14721370.13252674X-RAY DIFFRACTION100
4.16-4.580.12421410.12612680X-RAY DIFFRACTION100
4.58-5.240.15041470.13562697X-RAY DIFFRACTION100
5.24-6.60.18421260.1832774X-RAY DIFFRACTION100
6.6-95.80.18021660.16192908X-RAY DIFFRACTION99.81

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