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- PDB-6zh7: Crystal structure of fatty acid photodecarboxylase in the dark st... -

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Entry
Database: PDB / ID: 6zh7
TitleCrystal structure of fatty acid photodecarboxylase in the dark state determined by serial femtosecond crystallography at room temperature
ComponentsFatty acid photodecarboxylase, chloroplastic
KeywordsOXIDOREDUCTASE / photoenzyme / XFEL / radiation damage free
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHadjidemetriou, K. / Coquelle, N. / Weik, M. / Schlichting, I. / Barends, T.R.M. / Colletier, J.P.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0021 France
French National Research AgencyANR-15-CE32-0004 France
Citation
Journal: 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.
#1: Journal: 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. / 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
DepositionJun 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid photodecarboxylase, chloroplastic
B: Fatty acid photodecarboxylase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9428
Polymers122,2332
Non-polymers2,7096
Water7,098394
1
A: Fatty acid photodecarboxylase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4714
Polymers61,1171
Non-polymers1,3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid photodecarboxylase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4714
Polymers61,1171
Non-polymers1,3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.390, 60.010, 182.900
Angle α, β, γ (deg.)90.000, 90.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 77 - 643 / Label seq-ID: 1 - 567

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Fatty acid photodecarboxylase, chloroplastic / CvFAP


Mass: 61116.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella variabilis (plant) / Gene: FAP, CHLNCDRAFT_28598 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A248QE08, fatty acid photodecarboxylase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.76 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 281.15 K / Method: batch mode / pH: 5.5
Details: 19% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.5, 10 mM spermidine

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Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 93061 / % possible obs: 100 % / Redundancy: 355 % / CC1/2: 0.982 / CC star: 0.996 / R split: 0.151 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 236 % / Num. unique obs: 6086 / CC1/2: 0.548 / CC star: 0.841 / R split: 0.685 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRU

6yru


Resolution: 2→24.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.893 / SU ML: 0.151 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 4364 4.8 %RANDOM
Rwork0.1963 ---
obs0.198 85938 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.15 Å2 / Biso mean: 29.803 Å2 / Biso min: 11.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å2-1.56 Å2
2---1.19 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8417 0 166 394 8977
Biso mean--26.63 32.23 -
Num. residues----1125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139001
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178297
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.64812244
X-RAY DIFFRACTIONr_angle_other_deg1.2861.59719265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20651174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36521.473455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.944151412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9781571
X-RAY DIFFRACTIONr_chiral_restr0.0660.21147
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021906
Refine LS restraints NCS

Ens-ID: 1 / Number: 18263 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 340 -
Rwork0.308 6292 -
all-6632 -
obs--99.89 %

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