PDB-7qf5: Structure of the Q103L mutant of miniSOG

ID or keywords:

Entry

Database: PDB / ID: 7qf5

Title

Structure of the Q103L mutant of miniSOG

Components

miniSOG (Q103L mutant)

Keywords

FLAVOPROTEIN / LOV DOMAIN / RIBOFLAVIN / PHOTOSENSITIZING PROTEIN / FLUORESCENT PROTEIN

Function / homology

: / FLAVIN MONONUCLEOTIDE

Function and homology information

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.37 Å

Authors

Lafaye, C. / Aumonier, S. / von Stetten, D. / Noirclerc-Savoye, N. / Gotthard, G. / Royant, A.

Funding support

France, 1items

Citation

Journal: Photochem Photobiol Sci / Year: 2022
Title: Riboflavin-binding proteins for singlet oxygen production.
Authors: Lafaye, C. / Aumonier, S. / Torra, J. / Signor, L. / von Stetten, D. / Noirclerc-Savoye, M. / Shu, X. / Ruiz-Gonzalez, R. / Gotthard, G. / Royant, A. / Nonell, S.

History

Deposition	Dec 3, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2022	Group: Database references / Derived calculations / Category: atom_type / citation / citation_author Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7qf5.cif.gz	74.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qf5_validation.pdf.gz	814.6 KB	Display	wwPDB validaton report
Full document	7qf5_full_validation.pdf.gz	815.6 KB	Display
Data in XML	7qf5_validation.xml.gz	9 KB	Display
Data in CIF	7qf5_validation.cif.gz	12.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/7qf5 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qf5	HTTPS FTP

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Related structure data

Related structure data	7qf2C 7qf3C 7qf4C 6gpuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7qf4-d 6s46-d 6gpu-d 7qf3-d 1tiv-d 2yan-1 6qsa-d 3s5v-d 4ipc-d 2dly-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

AAA: miniSOG (Q103L mutant)

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	40.050, 40.050, 134.260
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

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Protein , 1 types, 1 molecules AAA

#1: Protein	miniSOG (Q103L mutant) Mass: 14869.806 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 5 types, 165 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris-Hcl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 15 mM CoCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9789 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2015 / Details: TOROIDAL MIRROR
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 1.37→38.38 Å / Num. obs: 23979 / % possible obs: 99.9 % / Redundancy: 8.3 % / B_iso Wilson estimate: 21.4 Å² / CC_1/2: 1 / R_rim(I) all: 0.06 / Net I/σ(I): 23.9
Reflection shell	Resolution: 1.37→1.41 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1734 / CC_1/2: 0.643 / R_rim(I) all: 1.07

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6GPU

6gpu

Resolution: 1.37→38.379 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.969 / SU B: 2.075 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1739	1152	4.804 %
R_work	0.1257	22827	-
all	0.128	-	-
obs	-	23979	99.937 %

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: 17.635 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.076 Å²	-0 Å²	-0 Å²
2-	-	0.076 Å²	-0 Å²
3-	-	-	-0.152 Å²

Refinement step

Cycle: LAST / Resolution: 1.37→38.379 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	938	0	34	161	1133

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1123
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1100
X-RAY DIFFRACTION	r_angle_refined_deg	1.62	1.651	1540
X-RAY DIFFRACTION	r_angle_other_deg	1.382	1.586	2544
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.562	5	144
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.885	21.97	66
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.602	15	211
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.202	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	146
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1280
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	262
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	200
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	923
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	483
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	456
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.219	0.2	96
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.031	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.007	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.217	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.254	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	1.587	1.544	514
X-RAY DIFFRACTION	r_mcbond_other	1.475	1.535	512
X-RAY DIFFRACTION	r_mcangle_it	1.997	2.317	648
X-RAY DIFFRACTION	r_mcangle_other	2.008	2.322	649
X-RAY DIFFRACTION	r_scbond_it	2.164	1.769	609
X-RAY DIFFRACTION	r_scbond_other	2.17	1.771	606
X-RAY DIFFRACTION	r_scangle_it	2.665	2.553	881
X-RAY DIFFRACTION	r_scangle_other	2.663	2.552	882
X-RAY DIFFRACTION	r_lrange_it	3.634	18.511	1275
X-RAY DIFFRACTION	r_lrange_other	3.366	17.87	1248
X-RAY DIFFRACTION	r_rigid_bond_restr	1.817	3	2223

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
1.37-1.406	0.253	98	0.226	1635	0.227	1736	0.86	0.878	99.8272	0.204
1.406-1.444	0.225	64	0.199	1632	0.201	1696	0.905	0.91	100	0.171
1.444-1.486	0.241	85	0.173	1543	0.177	1632	0.911	0.927	99.7549	0.147
1.486-1.531	0.186	63	0.142	1535	0.143	1598	0.94	0.955	100	0.114
1.531-1.582	0.174	73	0.129	1473	0.131	1546	0.947	0.963	100	0.102
1.582-1.637	0.182	71	0.113	1422	0.116	1493	0.961	0.97	100	0.09
1.637-1.699	0.151	81	0.11	1377	0.112	1459	0.967	0.975	99.9315	0.088
1.699-1.768	0.175	79	0.098	1317	0.102	1397	0.963	0.979	99.9284	0.077
1.768-1.846	0.155	71	0.09	1273	0.093	1344	0.97	0.982	100	0.073
1.846-1.936	0.167	52	0.093	1252	0.097	1304	0.976	0.982	100	0.077
1.936-2.041	0.139	61	0.093	1172	0.096	1234	0.975	0.983	99.919	0.077
2.041-2.164	0.185	44	0.101	1119	0.104	1164	0.968	0.984	99.9141	0.085
2.164-2.313	0.129	60	0.1	1058	0.101	1118	0.982	0.985	100	0.083
2.313-2.498	0.147	47	0.1	1003	0.102	1050	0.979	0.986	100	0.086
2.498-2.735	0.149	53	0.119	903	0.121	956	0.981	0.981	100	0.103
2.735-3.056	0.212	40	0.12	848	0.123	888	0.962	0.98	100	0.107
3.056-3.525	0.126	35	0.126	752	0.126	788	0.98	0.982	99.8731	0.12
3.525-4.308	0.166	34	0.118	650	0.121	684	0.977	0.984	100	0.119
4.308-6.054	0.158	19	0.15	533	0.151	552	0.981	0.982	100	0.155
6.054-38.379	0.335	22	0.252	330	0.256	353	0.946	0.944	99.7167	0.265

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