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- PDB-6ys1: Crystal structure of FAP R451K mutant in the dark at 100K -

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Basic information

Entry
Database: PDB / ID: 6ys1
TitleCrystal structure of FAP R451K mutant in the dark at 100K
ComponentsFatty acid Photodecarboxylase
KeywordsBIOSYNTHETIC PROTEIN / GMC fold
Function / homology
Function and homology information


fatty acid photodecarboxylase / oxidoreductase activity, acting on CH-OH group of donors / chloroplast / flavin adenine dinucleotide binding / lyase activity
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / STEARIC ACID / Fatty acid photodecarboxylase, chloroplastic
Similarity search - Component
Biological speciesChlorella variabilis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsSorigue, D. / Gotthard, G. / Blangy, S. / Nurizzo, D. / Royant, A. / Beisson, F. / Arnoux, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0021 France
CitationJournal: Science / Year: 2021
Title: Mechanism and dynamics of fatty acid photodecarboxylase.
Authors: Sorigue, D. / Hadjidemetriou, K. / Blangy, S. / Gotthard, G. / Bonvalet, A. / Coquelle, N. / Samire, P. / Aleksandrov, A. / Antonucci, L. / Benachir, A. / Boutet, S. / Byrdin, M. / ...Authors: Sorigue, D. / Hadjidemetriou, K. / Blangy, S. / Gotthard, G. / Bonvalet, A. / Coquelle, N. / Samire, P. / Aleksandrov, A. / Antonucci, L. / Benachir, A. / Boutet, S. / Byrdin, M. / Cammarata, M. / Carbajo, S. / Cuine, S. / Doak, R.B. / Foucar, L. / Gorel, A. / Grunbein, M. / Hartmann, E. / Hienerwadel, R. / Hilpert, M. / Kloos, M. / Lane, T.J. / Legeret, B. / Legrand, P. / Li-Beisson, Y. / Moulin, S.L.Y. / Nurizzo, D. / Peltier, G. / Schiro, G. / Shoeman, R.L. / Sliwa, M. / Solinas, X. / Zhuang, B. / Barends, T.R.M. / Colletier, J.P. / Joffre, M. / Royant, A. / Berthomieu, C. / Weik, M. / Domratcheva, T. / Brettel, K. / Vos, M.H. / Schlichting, I. / Arnoux, P. / Muller, P. / Beisson, F.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6075
Polymers61,0591
Non-polymers1,5494
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint0 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.620, 102.780, 155.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Fatty acid Photodecarboxylase


Mass: 61058.551 Da / Num. of mol.: 1 / Mutation: R451K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella variabilis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D0TC92
#2: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2 / 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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.64→90 Å / Num. obs: 87644 / % possible obs: 99.5 % / Redundancy: 4.232 % / Biso Wilson estimate: 28.854 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.083 / Χ2: 1.019 / Net I/σ(I): 12.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.64-1.754.0410.8531.52153470.5370.98499.5
1.75-1.894.430.4942.85147870.8040.56399.9
1.89-2.074.3710.2575.47136460.9350.29499.7
2.07-2.324.0810.1449.32125530.9750.16699.6
2.32-2.674.2730.08515.47106480.9910.09799.3
2.67-3.274.3790.05323.7493250.9970.0699.7
3.27-4.623.940.03135.4171980.9980.03698.7
4.62-904.3040.02541.8341400.9990.02898.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRU

6yru


Resolution: 1.64→46.401 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.979 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1921 4341 4.954 %
Rwork0.1661 --
all0.167 --
obs-87633 99.468 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.878 Å2
Baniso -1Baniso -2Baniso -3
1-0.818 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.557 Å2
Refinement stepCycle: LAST / Resolution: 1.64→46.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 106 365 4725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134506
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174180
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.6426119
X-RAY DIFFRACTIONr_angle_other_deg1.5271.5759710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9595587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96121.598219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26715697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1721533
X-RAY DIFFRACTIONr_chiral_restr0.090.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02936
X-RAY DIFFRACTIONr_nbd_refined0.2070.2897
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24038
X-RAY DIFFRACTIONr_nbtor_refined0.170.22198
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2334
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.222
X-RAY DIFFRACTIONr_nbd_other0.2540.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4750.221
X-RAY DIFFRACTIONr_mcbond_it1.7912.2232303
X-RAY DIFFRACTIONr_mcbond_other1.7852.2212302
X-RAY DIFFRACTIONr_mcangle_it2.3873.3252881
X-RAY DIFFRACTIONr_mcangle_other2.3873.3262882
X-RAY DIFFRACTIONr_scbond_it3.2332.5332203
X-RAY DIFFRACTIONr_scbond_other3.2332.5342204
X-RAY DIFFRACTIONr_scangle_it4.7613.6553230
X-RAY DIFFRACTIONr_scangle_other4.763.6563231
X-RAY DIFFRACTIONr_lrange_it5.61227.0015107
X-RAY DIFFRACTIONr_lrange_other5.52226.6145015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6830.323160.3016105X-RAY DIFFRACTION99.5967
1.683-1.7290.3092940.2775921X-RAY DIFFRACTION98.965
1.729-1.7790.2682890.255823X-RAY DIFFRACTION99.8204
1.779-1.8330.2682780.2245660X-RAY DIFFRACTION99.9327
1.833-1.8940.2353040.2025443X-RAY DIFFRACTION99.809
1.894-1.960.2282740.1935311X-RAY DIFFRACTION99.8391
1.96-2.0340.2012770.1735106X-RAY DIFFRACTION99.6667
2.034-2.1170.1862600.1634910X-RAY DIFFRACTION99.653
2.117-2.2110.1882200.1574749X-RAY DIFFRACTION99.4795
2.211-2.3190.192460.1514489X-RAY DIFFRACTION99.7262
2.319-2.4440.1792180.1444289X-RAY DIFFRACTION98.7944
2.444-2.5920.1792560.1414047X-RAY DIFFRACTION99.7219
2.592-2.7710.1831930.1493849X-RAY DIFFRACTION99.8518
2.771-2.9930.1891820.1533590X-RAY DIFFRACTION99.762
2.993-3.2780.1891600.1653326X-RAY DIFFRACTION99.5147
3.278-3.6640.1751720.1632967X-RAY DIFFRACTION99.2726
3.664-4.230.1641370.142640X-RAY DIFFRACTION98.4054
4.23-5.1780.1331000.1332266X-RAY DIFFRACTION97.971
5.178-7.3090.236980.1671782X-RAY DIFFRACTION99.7347
7.309-460.15670.1751019X-RAY DIFFRACTION97.8378

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