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- PDB-7r33: Difference-refined structure of fatty acid photodecarboxylase 20 ... -

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Basic information

Entry
Database: PDB / ID: 7r33
TitleDifference-refined structure of fatty acid photodecarboxylase 20 ps 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 / 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. / 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 1.1Dec 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jan 31, 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

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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: 93060 / % possible obs: 100 % / Redundancy: 461 % / CC star: 0.996 / R split: 0.134 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 236 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6086 / CC star: 0.869 / R split: 0.613 / % 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→10 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 38.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3201 4478 5 %
Rwork0.2643 85090 -
obs0.2671 89568 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.37 Å2 / Biso mean: 34.2289 Å2 / Biso min: 8.49 Å2
Refinement stepCycle: final / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8417 0 166 394 8977
Biso mean--27.95 35.09 -
Num. residues----1125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.020.44911520.401627362888
2.02-2.050.45071650.394428983063
2.05-2.070.42571430.37428142957
2.07-2.10.44711460.366627952941
2.1-2.120.44421330.364228232956
2.12-2.150.41641300.375128172947
2.15-2.180.41351440.365628272971
2.18-2.220.3871560.352828212977
2.22-2.250.38681300.336328602990
2.25-2.290.40661420.343528212963
2.29-2.330.37811480.356328252973
2.33-2.370.4441580.363928282986
2.37-2.410.39411770.349727922969
2.41-2.460.45031390.33828512990
2.46-2.510.37411370.326228052942
2.51-2.570.37651490.325428432992
2.57-2.630.38211540.323628262980
2.63-2.70.38791590.318628322991
2.7-2.780.39011500.312928322982
2.78-2.870.38061460.292828482994
2.87-2.970.32461570.276628252982
2.97-3.080.35821590.26728222981
3.08-3.220.33641600.266428132973
3.22-3.380.33141590.242228402999
3.38-3.590.23071450.213428803025
3.59-3.850.25771660.212628182984
3.85-4.210.26331560.206528523008
4.21-4.760.21321360.16929003036
4.76-5.80.18991270.172228983025
5.8-100.20071550.16229483103

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