PDB-6yrv: Crystal structure of FAP after illumination at 100K

ID or keywords:

Entry

Database: PDB / ID: 6yrv

Title

Crystal structure of FAP after illumination at 100K

Components

Fatty acid Photodecarboxylase

Keywords

BIOSYNTHETIC PROTEIN / GMC fold

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

Biological species

Chlorella variabilis (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.94 Å

Authors

Sorigue, D. / Gotthard, G. / Blangy, S. / Nurizzo, D. / Royant, A. / 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	6yrv.cif.gz	143.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6yrv.ent.gz		Display	PDB format
PDBx/mmJSON format	6yrv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	6yruSC 6yrxC 6yrzC 6ys1C 6ys2C 6zh7C 7av4C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6yru-d 6ys1-d 4o0c-d 4o48-d 4lvu-d 4pu6-d 4osy-d 4osx-d 3rro-d 6jbw-2 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

hetero molecules

62.4 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

Unit cell

Length a, b, c (Å)	89.960, 103.860, 156.300
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 / Mass: 61086.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella variabilis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D0TC92

-
Non-polymers , 5 types, 528 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-PJ8 / heptadecane / 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 / Carbon dioxide Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO₂
#5: Chemical	ChemComp-STE / STEARIC ACID / Stearic acid Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 524 / 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: 3.01 Å³/Da / Density % sol: 59.12 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.97372 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 10, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97372 Å / Relative weight: 1

Reflection

Resolution: 1.94→86.5 Å / Num. obs: 54600 / % possible obs: 100 % / Redundancy: 6.585 % / B_iso Wilson estimate: 34.131 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.106 / R_rim(I) all: 0.116 / Χ²: 1.02 / Net I/σ(I): 11.62

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
1.94-1.99	6.525	0.78	2.23	3961	0.724	0.849	100
1.99-2.04	6.817	0.638	2.94	3924	0.845	0.691	100
2.04-2.1	6.695	0.522	3.7	3761	0.9	0.568	100
2.1-2.17	6.596	0.441	4.38	3728	0.927	0.48	100
2.17-2.24	6.317	0.37	5.22	3532	0.941	0.404	99.9
2.24-2.32	6.47	0.312	6.13	3482	0.966	0.339	100
2.32-2.4	6.892	0.262	7.57	3329	0.973	0.284	100
2.4-2.5	6.87	0.23	8.58	3233	0.979	0.249	100
2.5-2.61	6.725	0.201	9.65	3079	0.983	0.218	100
2.61-2.74	6.339	0.177	10.73	2980	0.983	0.193	100
2.74-2.89	6.679	0.147	13	2815	0.989	0.16	100
2.89-3.06	6.847	0.121	15.38	2668	0.993	0.131	100
3.06-3.28	6.675	0.096	18.63	2510	0.994	0.104	100
3.28-3.54	6.284	0.077	21.67	2338	0.995	0.084	99.9
3.54-3.88	6.421	0.065	24.66	2184	0.996	0.071	99.9
3.88-4.33	6.611	0.057	27.61	1973	0.997	0.062	99.8
4.33-5	6.352	0.05	28.83	1751	0.997	0.055	99.8
5-6.13	6.227	0.052	26.72	1486	0.998	0.057	99.9
6.13-8.67	6.468	0.045	29.16	1182	0.998	0.049	100
8.67-86	5.804	0.033	31.65	684	0.999	0.036	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: 1.94→86 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.955 / SU B: 3.572 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2033	2828	5.193 %
R_work	0.1651	-	-
all	0.167	-	-
obs	-	54459	99.96 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 29.774 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.984 Å²	0 Å²	0 Å²
2-	-	0.631 Å²	0 Å²
3-	-	-	-1.615 Å²

Refinement step

Cycle: LAST / Resolution: 1.94→86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4267	0	93	524	4884

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	4450
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	4113
X-RAY DIFFRACTION	r_angle_refined_deg	1.697	1.648	6034
X-RAY DIFFRACTION	r_angle_other_deg	1.443	1.602	9539
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.441	5	572
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.16	21.667	216
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.333	15	682
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.441	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	567
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	5069
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	924
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	925
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	4120
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	2225
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	2128
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.222	0.2	476
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.091	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.29	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.255	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	2.452	2.955	2291
X-RAY DIFFRACTION	r_mcbond_other	2.45	2.954	2290
X-RAY DIFFRACTION	r_mcangle_it	3.372	4.422	2862
X-RAY DIFFRACTION	r_mcangle_other	3.372	4.423	2863
X-RAY DIFFRACTION	r_scbond_it	3.416	3.207	2159
X-RAY DIFFRACTION	r_scbond_other	3.416	3.208	2160
X-RAY DIFFRACTION	r_scangle_it	5.02	4.68	3172
X-RAY DIFFRACTION	r_scangle_other	5.02	4.681	3173
X-RAY DIFFRACTION	r_lrange_it	12.909	36.828	5246
X-RAY DIFFRACTION	r_lrange_other	12.39	36.029	5085

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.94-1.99	0.292	227	0.261	3764	0.263	3991	0.825	0.849	100	0.257
1.99-2.045	0.3	205	0.24	3688	0.243	3894	0.852	0.869	99.9743	0.236
2.045-2.104	0.267	185	0.215	3562	0.217	3747	0.867	0.892	100	0.206
2.104-2.169	0.225	183	0.196	3520	0.198	3703	0.888	0.905	100	0.183
2.169-2.24	0.246	183	0.199	3340	0.201	3525	0.874	0.897	99.9433	0.184
2.24-2.318	0.248	210	0.186	3258	0.19	3468	0.891	0.908	100	0.168
2.318-2.406	0.208	169	0.178	3158	0.179	3327	0.912	0.923	100	0.157
2.406-2.504	0.224	180	0.17	3030	0.173	3211	0.925	0.929	99.9689	0.144
2.504-2.615	0.203	135	0.165	2931	0.166	3066	0.936	0.94	100	0.138
2.615-2.743	0.241	156	0.167	2809	0.171	2966	0.915	0.939	99.9663	0.143
2.743-2.891	0.179	141	0.154	2669	0.155	2811	0.95	0.957	99.9644	0.132
2.891-3.066	0.228	141	0.176	2518	0.179	2660	0.935	0.944	99.9624	0.159
3.066-3.278	0.224	128	0.17	2372	0.173	2500	0.946	0.956	100	0.162
3.278-3.54	0.175	121	0.165	2208	0.166	2332	0.97	0.966	99.8714	0.161
3.54-3.877	0.189	119	0.143	2061	0.145	2182	0.958	0.974	99.9083	0.144
3.877-4.334	0.155	88	0.123	1887	0.125	1979	0.972	0.977	99.7979	0.131
4.334-5.002	0.161	89	0.117	1655	0.12	1747	0.972	0.982	99.8283	0.129
5.002-6.121	0.176	66	0.153	1421	0.154	1488	0.975	0.978	99.9328	0.16
6.121-8.635	0.178	66	0.152	1110	0.154	1176	0.957	0.971	100	0.164
8.635-86.503	0.131	35	0.186	658	0.183	695	0.977	0.962	99.7122	0.227

-
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 , 5 types, 528 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 , 5 types, 528 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 , 5 types, 528 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