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- PDB-5ncc: Structure of Fatty acid Photodecarboxylase in complex with FAD an... -

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Basic information

Entry
Database: PDB / ID: 5ncc
TitleStructure of Fatty acid Photodecarboxylase in complex with FAD and palmitic acid
ComponentsFatty acid Photodecarboxylase
KeywordsOXIDOREDUCTASE
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 / PALMITIC ACID / Fatty acid photodecarboxylase, chloroplastic
Similarity search - Component
Biological speciesChlorella variabilis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsArnoux, P. / Sorigue, D. / Beisson, F. / Pignol, D.
Citation
Journal: Science / Year: 2017
Title: An algal photoenzyme converts fatty acids to hydrocarbons.
Authors: Sorigue, D. / Legeret, B. / Cuine, S. / Blangy, S. / Moulin, S. / Billon, E. / Richaud, P. / Brugiere, S. / Coute, Y. / Nurizzo, D. / Muller, P. / Brettel, K. / Pignol, D. / Arnoux, P. / Li- ...Authors: Sorigue, D. / Legeret, B. / Cuine, S. / Blangy, S. / Moulin, S. / Billon, E. / Richaud, P. / Brugiere, S. / Coute, Y. / Nurizzo, D. / Muller, P. / Brettel, K. / Pignol, D. / Arnoux, P. / Li-Beisson, Y. / Peltier, G. / Beisson, F.
#1: Journal: To Be Published
Title: Structure of Alkane photosynthase
Authors: Sorigue, D. / Arnoux, P. / Pignol, D. / Beisson, F.
History
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid Photodecarboxylase
B: Fatty acid Photodecarboxylase
C: Fatty acid Photodecarboxylase
D: Fatty acid Photodecarboxylase
E: Fatty acid Photodecarboxylase
F: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,14516
Polymers376,4066
Non-polymers5,73910
Water00
1
A: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7763
Polymers62,7341
Non-polymers1,0422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7763
Polymers62,7341
Non-polymers1,0422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7763
Polymers62,7341
Non-polymers1,0422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7763
Polymers62,7341
Non-polymers1,0422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5202
Polymers62,7341
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fatty acid Photodecarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5202
Polymers62,7341
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.234, 192.109, 116.127
Angle α, β, γ (deg.)90.00, 113.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23C
14A
24C
15A
25D
16A
26D
17A
27E
18A
28E
19A
29F
110A
210F
111B
211C
112B
212D
113B
213E
114B
214F
115B
215C
116B
216D
117B
217E
118B
218F
119C
219D
120C
220E
121C
221F
122C
222D
123C
223E
124C
224F
125D
225E
126D
226F
127D
227E
128D
228F
129E
229F
130E
230F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERHISHISAA61 - 4031 - 343
21SERSERHISHISBB61 - 4031 - 343
12GLYGLYALAALAAA409 - 644349 - 584
22GLYGLYALAALABB409 - 644349 - 584
13SERSERHISHISAA61 - 4031 - 343
23SERSERHISHISCC61 - 4031 - 343
14GLYGLYALAALAAA409 - 644349 - 584
24GLYGLYALAALACC409 - 644349 - 584
15SERSERHISHISAA61 - 4031 - 343
25SERSERHISHISDD61 - 4031 - 343
16GLYGLYALAALAAA409 - 644349 - 584
26GLYGLYALAALADD409 - 644349 - 584
17SERSERHISHISAA61 - 4031 - 343
27SERSERHISHISEE61 - 4031 - 343
18GLYGLYALAALAAA409 - 644349 - 584
28GLYGLYALAALAEE409 - 644349 - 584
19SERSERHISHISAA61 - 4031 - 343
29SERSERHISHISFF61 - 4031 - 343
110GLYGLYALAALAAA409 - 644349 - 584
210GLYGLYALAALAFF409 - 644349 - 584
111SERSERILEILEBB61 - 4041 - 344
211SERSERILEILECC61 - 4041 - 344
112SERSERILEILEBB61 - 4041 - 344
212SERSERILEILEDD61 - 4041 - 344
113SERSERILEILEBB61 - 4041 - 344
213SERSERILEILEEE61 - 4041 - 344
114SERSERILEILEBB61 - 4041 - 344
214SERSERILEILEFF61 - 4041 - 344
115GLYGLYSERSERBB409 - 645349 - 585
215GLYGLYSERSERCC409 - 645349 - 585
116GLYGLYSERSERBB409 - 645349 - 585
216GLYGLYSERSERDD409 - 645349 - 585
117GLYGLYSERSERBB409 - 645349 - 585
217GLYGLYSERSEREE409 - 645349 - 585
118GLYGLYSERSERBB409 - 645349 - 585
218GLYGLYSERSERFF409 - 645349 - 585
119SERSERILEILECC61 - 4041 - 344
219SERSERILEILEDD61 - 4041 - 344
120SERSERILEILECC61 - 4041 - 344
220SERSERILEILEEE61 - 4041 - 344
121SERSERILEILECC61 - 4041 - 344
221SERSERILEILEFF61 - 4041 - 344
122GLYGLYSERSERCC409 - 645349 - 585
222GLYGLYSERSERDD409 - 645349 - 585
123GLYGLYSERSERCC409 - 645349 - 585
223GLYGLYSERSEREE409 - 645349 - 585
124GLYGLYSERSERCC409 - 645349 - 585
224GLYGLYSERSERFF409 - 645349 - 585
125SERSERILEILEDD61 - 4041 - 344
225SERSERILEILEEE61 - 4041 - 344
126SERSERILEILEDD61 - 4041 - 344
226SERSERILEILEFF61 - 4041 - 344
127GLYGLYSERSERDD409 - 645349 - 585
227GLYGLYSERSEREE409 - 645349 - 585
128GLYGLYSERSERDD409 - 645349 - 585
228GLYGLYSERSERFF409 - 645349 - 585
129SERSERILEILEEE61 - 4041 - 344
229SERSERILEILEFF61 - 4041 - 344
130GLYGLYSERSEREE409 - 645349 - 585
230GLYGLYSERSERFF409 - 645349 - 585

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

#1: Protein
Fatty acid Photodecarboxylase


Mass: 62734.371 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella variabilis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A248QE08*PLUS
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 20-25% PEG3350 17-20% 2-propanol 0.1M NaCitrate 0.1M pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.853
11H, -K, -H-L20.147
ReflectionResolution: 3.12→100 Å / Num. obs: 70398 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 6.4
Reflection shellResolution: 3.12→3.26 Å / Rmerge(I) obs: 0.772

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JBV

2jbv


Resolution: 3.12→49.07 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.831 / SU B: 20.007 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27827 5521 8.5 %RANDOM
Rwork0.22463 ---
obs0.22886 59378 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.396 Å2
Baniso -1Baniso -2Baniso -3
1--26.9 Å20 Å2-22.22 Å2
2--20.14 Å20 Å2
3---6.75 Å2
Refinement stepCycle: 1 / Resolution: 3.12→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25794 0 390 0 26184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01926714
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.97836260
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.10653450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07823.6071098
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.125154152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.84415198
X-RAY DIFFRACTIONr_chiral_restr0.130.23996
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7046.14413854
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.6989.20517286
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2996.09112860
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.33495.47846985
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A193360.07
12B193360.07
21A132680.06
22B132680.06
31A192760.07
32C192760.07
41A132660.05
42C132660.05
51A193120.08
52D193120.08
61A132560.06
62D132560.06
71A191880.08
72E191880.08
81A130980.07
82E130980.07
91A192200.08
92F192200.08
101A130300.08
102F130300.08
111B193520.08
112C193520.08
121B193160.08
122D193160.08
131B192280.08
132E192280.08
141B192100.08
142F192100.08
151B132680.06
152C132680.06
161B132820.07
162D132820.07
171B130820.08
172E130820.08
181B130560.08
182F130560.08
191C193480.08
192D193480.08
201C192520.08
202E192520.08
211C192300.08
212F192300.08
221C133080.06
222D133080.06
231C131100.08
232E131100.08
241C130840.07
242F130840.07
251D192080.08
252E192080.08
261D191880.08
262F191880.08
271D131740.08
272E131740.08
281D131020.07
282F131020.07
291E191760.08
292F191760.08
301E128860.09
302F128860.09
LS refinement shellResolution: 3.123→3.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 269 -
Rwork0.262 2658 -
obs--59.1 %

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