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- PDB-7r36: Difference-refined structure of fatty acid photodecarboxylase 2 m... -

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Basic information

Entry
Database: PDB / ID: 7r36
TitleDifference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX
ComponentsFatty acid photodecarboxylase, chloroplastic
KeywordsOXIDOREDUCTASE / Fatty acid decarboxylation
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHadjidemetriou, K. / Coquelle, N. / Barends, T.R.M. / De Zitter, E. / Schlichting, I. / Colletier, J.P. / Weik, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned.
Authors: Hadjidemetriou, K. / Coquelle, N. / Barends, T.R.M. / De Zitter, E. / Schlichting, I. / Colletier, J.P. / Weik, M.
History
DepositionFeb 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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

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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 / 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 / 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 / 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: 2.2→25 Å / Num. obs: 70385 / % possible obs: 100 % / Redundancy: 115 % / CC star: 0.983 / R split: 0.249 / Net I/σ(I): 3.7
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 82 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4671 / CC star: 0.816 / R split: 0.678 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
CrystFELv.0.8.0data reduction
CrystFELv.0.8.0data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZH7

6zh7


Resolution: 2.2→10 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.57 / Phase error: 46.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.379 3362 5 %
Rwork0.2969 63886 -
obs0.301 67248 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.42 Å2 / Biso mean: 34.3506 Å2 / Biso min: 5.91 Å2
Refinement stepCycle: final / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8417 0 160 394 8971
Biso mean--27.33 31.56 -
Num. residues----1125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.230.48031400.41626072747
2.23-2.260.45141400.398326362776
2.26-2.30.41851440.388326272771
2.3-2.340.44891250.375426562781
2.34-2.380.41631610.377626632824
2.38-2.420.45241310.392826122743
2.42-2.460.41521330.376626782811
2.46-2.510.4691380.380926412779
2.51-2.570.47191480.383926402788
2.57-2.630.46971410.374526392780
2.63-2.690.46211240.366226982822
2.69-2.760.43171450.383526482793
2.76-2.840.45531660.3626372803
2.84-2.930.44161320.363126592791
2.93-3.030.43781480.340526352783
3.03-3.150.36331480.322126652813
3.15-3.290.42111170.291626742791
3.29-3.460.38711400.259926772817
3.46-3.660.34731300.243926652795
3.66-3.930.33081480.260226712819
3.93-4.30.33741390.254127172856
4.3-4.850.30541290.213726792808
4.85-5.90.30751400.216327182858
5.9-100.26371550.210827442899

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