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- PDB-6ys2: Crystal structure of FAP R451A in the dark at 100K -

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Basic information

Entry
Database: PDB / ID: 6ys2
TitleCrystal structure of FAP R451A in the dark at 100K
ComponentsFatty acid Photodecarboxylase
KeywordsBIOSYNTHETIC PROTEIN / GMC fold
Function / homology
Function and homology information


fatty acid photodecarboxylase / choline dehydrogenase activity / glycine betaine biosynthetic process from choline / chloroplast / flavin adenine dinucleotide binding / lyase activity / membrane
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: 1.97 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)62,3554
Polymers61,0001
Non-polymers1,3553
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-6 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.950, 60.820, 180.150
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 Fatty acid Photodecarboxylase


Mass: 61000.449 Da / Num. of mol.: 1 / Mutation: R451A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
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: 0.97625 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.97→86 Å / Num. obs: 46463 / % possible obs: 99.5 % / Redundancy: 4.848 % / Biso Wilson estimate: 33.757 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.15 / Χ2: 0.94 / Net I/σ(I): 8.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.97-2.094.8711.011.4473840.5681.13199
2.09-2.234.7190.6982.1268160.7140.78499.8
2.23-2.414.7870.4463.2565360.8740.49999.1
2.41-2.645.080.3084.960610.9370.34399.7
2.64-2.954.9290.1947.4354700.9740.21799.5
2.95-3.414.980.11212.3549090.9910.12599.9
3.41-4.174.8420.06120.341140.9970.06899.5
4.17-5.874.7890.04625.5332580.9980.05199.6
5.87-864.240.04227.9619150.9980.04798.4

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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: 1.97→49.375 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.737 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2287 2425 5.22 %
Rwork0.182 --
all0.184 --
obs-46460 99.448 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.043 Å2
Baniso -1Baniso -2Baniso -3
1--1.225 Å20 Å20 Å2
2--1.164 Å20 Å2
3---0.061 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 93 314 4599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174075
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6425951
X-RAY DIFFRACTIONr_angle_other_deg1.3321.5749457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7185559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65921.737213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6821531
X-RAY DIFFRACTIONr_chiral_restr0.0770.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_nbd_refined0.1960.2929
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24019
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22109
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2338
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.211
X-RAY DIFFRACTIONr_nbd_other0.2230.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.212
X-RAY DIFFRACTIONr_mcbond_it2.5523.3992242
X-RAY DIFFRACTIONr_mcbond_other2.5443.3982241
X-RAY DIFFRACTIONr_mcangle_it3.5515.0872799
X-RAY DIFFRACTIONr_mcangle_other3.5525.0892800
X-RAY DIFFRACTIONr_scbond_it3.0543.6092151
X-RAY DIFFRACTIONr_scbond_other3.0543.612148
X-RAY DIFFRACTIONr_scangle_it4.6115.33152
X-RAY DIFFRACTIONr_scangle_other4.615.2993153
X-RAY DIFFRACTIONr_lrange_it6.5740.3374987
X-RAY DIFFRACTIONr_lrange_other6.49640.1434922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0210.341850.3053134X-RAY DIFFRACTION98.2825
2.021-2.0770.3281540.2743157X-RAY DIFFRACTION99.8793
2.077-2.1370.2581670.2513048X-RAY DIFFRACTION99.9689
2.137-2.2030.2791370.2472974X-RAY DIFFRACTION99.6477
2.203-2.2750.2611540.232908X-RAY DIFFRACTION99.7719
2.275-2.3550.2591480.2142770X-RAY DIFFRACTION98.4813
2.355-2.4430.2521820.1962649X-RAY DIFFRACTION99.7182
2.443-2.5430.2171530.1772593X-RAY DIFFRACTION99.7457
2.543-2.6560.2651390.1792507X-RAY DIFFRACTION99.661
2.656-2.7860.2191300.1822374X-RAY DIFFRACTION100
2.786-2.9360.2291380.1792272X-RAY DIFFRACTION99.3814
2.936-3.1140.2641310.1932138X-RAY DIFFRACTION99.4739
3.114-3.3290.231080.1792037X-RAY DIFFRACTION99.8603
3.329-3.5950.2091090.1771906X-RAY DIFFRACTION99.9008
3.595-3.9380.1891030.1521747X-RAY DIFFRACTION99.4624
3.938-4.4010.185790.1391605X-RAY DIFFRACTION99.2339
4.401-5.080.159610.1281454X-RAY DIFFRACTION99.5401
5.08-6.2170.219530.1561232X-RAY DIFFRACTION99.6897
6.217-8.7710.226570.15967X-RAY DIFFRACTION99.1288
8.771-490.199370.171563X-RAY DIFFRACTION96.6184

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