PDB-6yrz: Crystal structure of FAP et pH 8.5 after illumination at 150K

ID or keywords:

Entry

Database: PDB / ID: 6yrz

Title

Crystal structure of FAP et pH 8.5 after illumination at 150K

Components

Fatty acid photodecarboxylase, chloroplastic

Keywords

BIOSYNTHETIC 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

Biological species

Chlorella variabilis (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.824 Å

Authors

Sorigue, D. / Legrand, P. / Blangy, S. / Beisson, F. / Arnoux, P.

Funding support

France, 1items

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. / ...

History

Deposition	Apr 20, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2023	Group: 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 1.2	Jan 24, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6yrz.cif.gz	141.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6yrz.ent.gz		Display	PDB format
PDBx/mmJSON format	6yrz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yr/6yrz ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yrz	HTTPS FTP

-
Related structure data

Related structure data	6yruSC 6yrvC 6yrxC 6ys1C 6ys2C 6zh7C 7av4C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ys2-d 6zh7-2 7av4-d 6zh7-1 6yrx-d 5l9y-d 4mjw-2 5guw-1 4f7b-4 2a8j-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.11577/1775333 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#77 - May 2006 Glucose Oxidase similarity (6) #37 - Jan 2003 Serum Albumin similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

AAA: Fatty acid photodecarboxylase, chloroplastic

hetero molecules

62.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, monomer

Unit cell

Length a, b, c (Å)	90.470, 104.560, 156.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

-
Protein , 1 types, 1 molecules AAA

#1: Protein	Fatty acid photodecarboxylase, chloroplastic / CvFAP Mass: 61086.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella variabilis (plant) / Gene: FAP, CHLNCDRAFT_28598 / Production host: Escherichia coli (E. coli) References: UniProt: A0A248QE08, fatty acid photodecarboxylase

-
Non-polymers , 6 types, 445 molecules

#2: 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
#3: Chemical	ChemComp-PJ8 / heptadecane Mass: 240.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₃₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CO2 / CARBON DIOXIDE Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO₂
#5: Chemical	ChemComp-STE / STEARIC ACID Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₆O₂
#6: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 59.5 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM

-
Data collection

Diffraction

Mean temperature: 150 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 28, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.82→87 Å / Num. obs: 66267 / % possible obs: 99.7 % / Redundancy: 13.518 % / B_iso Wilson estimate: 37.236 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.086 / R_rim(I) all: 0.089 / Χ²: 1.188 / Net I/σ(I): 18.38

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.82-1.93	13.489	1.038	2.09	10478	0.816	1.078	98.2
1.93-2.07	13.356	0.615	3.79	9959	0.929	0.639	100
2.07-2.23	13.738	0.361	6.84	9361	0.973	0.375	100
2.23-2.45	14.226	0.214	11.37	8606	0.991	0.222	100
2.45-2.73	13.801	0.143	16.98	7750	0.996	0.149	100
2.73-3.15	13.095	0.092	26.13	6923	0.998	0.096	100
3.15-3.86	13.653	0.056	44.53	5898	0.999	0.058	100
3.86-5.44	12.643	0.044	56.62	4614	0.999	0.046	100
5.44-87	12.671	0.036	59.83	2678	0.999	0.038	99.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6YRU

6yru

Resolution: 1.824→46.819 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.966 / WR_factor R_free: 0.182 / WR_factor R_work: 0.152 / SU B: 2.564 / SU ML: 0.074 / Average fsc free: 0.9205 / Average fsc work: 0.931 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1881	3312	4.998 %
R_work	0.1583	62955	-
all	0.16	-	-
obs	-	66267	99.666 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 33.727 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.011 Å²	0 Å²	0 Å²
2-	-	-0.024 Å²	0 Å²
3-	-	-	0.013 Å²

Refinement step

Cycle: LAST / Resolution: 1.824→46.819 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4216	0	109	440	4765

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	4434
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	4111
X-RAY DIFFRACTION	r_angle_refined_deg	1.728	1.645	6007
X-RAY DIFFRACTION	r_angle_other_deg	1.465	1.589	9536
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.397	5	568
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.17	21.455	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.923	15	684
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.822	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	562
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	5031
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	928
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	864
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	3954
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	2137
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	2114
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	365
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.215	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.263	0.2	36
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.311	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	2.975	3.362	2260
X-RAY DIFFRACTION	r_mcbond_other	2.973	3.36	2259
X-RAY DIFFRACTION	r_mcangle_it	3.632	5.024	2823
X-RAY DIFFRACTION	r_mcangle_other	3.632	5.027	2824
X-RAY DIFFRACTION	r_scbond_it	3.947	3.704	2174
X-RAY DIFFRACTION	r_scbond_other	3.946	3.705	2175
X-RAY DIFFRACTION	r_scangle_it	5.756	5.387	3181
X-RAY DIFFRACTION	r_scangle_other	5.755	5.388	3182
X-RAY DIFFRACTION	r_lrange_it	6.887	40.667	5029
X-RAY DIFFRACTION	r_lrange_other	6.784	40.082	4921

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.824-1.871	0.363	232	0.345	4479	X-RAY DIFFRACTION	95.947
1.871-1.922	0.331	230	0.283	4503	X-RAY DIFFRACTION	100
1.922-1.978	0.277	229	0.235	4367	X-RAY DIFFRACTION	100
1.978-2.039	0.231	226	0.203	4247	X-RAY DIFFRACTION	100
2.039-2.106	0.209	216	0.178	4151	X-RAY DIFFRACTION	100
2.106-2.18	0.202	207	0.168	4008	X-RAY DIFFRACTION	100
2.18-2.262	0.214	208	0.156	3847	X-RAY DIFFRACTION	100
2.262-2.354	0.207	199	0.157	3691	X-RAY DIFFRACTION	100
2.354-2.459	0.178	207	0.14	3558	X-RAY DIFFRACTION	100
2.459-2.579	0.193	169	0.144	3437	X-RAY DIFFRACTION	100
2.579-2.718	0.179	192	0.139	3223	X-RAY DIFFRACTION	100
2.718-2.883	0.186	170	0.144	3113	X-RAY DIFFRACTION	99.9696
2.883-3.081	0.192	132	0.151	2923	X-RAY DIFFRACTION	100
3.081-3.328	0.201	151	0.17	2683	X-RAY DIFFRACTION	100
3.328-3.645	0.182	139	0.165	2503	X-RAY DIFFRACTION	99.9622
3.645-4.074	0.172	102	0.145	2296	X-RAY DIFFRACTION	100
4.074-4.703	0.125	103	0.115	2034	X-RAY DIFFRACTION	100
4.703-5.756	0.164	76	0.134	1736	X-RAY DIFFRACTION	100
5.756-8.122	0.181	79	0.166	1359	X-RAY DIFFRACTION	99.9305
8.122-46.8	0.171	45	0.179	797	X-RAY DIFFRACTION	99.1755

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules AAA

-
Non-polymers , 6 types, 445 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 1 molecules AAA

-Non-polymers , 6 types, 445 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules AAA

-
Non-polymers , 6 types, 445 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi