PDB-7qf3: Structure of the R57Q mutant of miniSOG expressed in E. coli in r...

ID or keywords:

Entry

Database: PDB / ID: 7qf3

Title

Structure of the R57Q mutant of miniSOG expressed in E. coli in regular LB medium

Components

miniSOG (R57Q 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: 1.1 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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Download

PDBx/mmCIF format	7qf3.cif.gz	71.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7qf3.ent.gz		Display	PDB format
PDBx/mmJSON format	7qf3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/7qf3 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qf3	HTTPS FTP

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Related structure data

Related structure data	7qf2C 7qf4C 7qf5C 6gpuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7qf4-d 7qf2-d 6gpu-d 7qf5-d 6s45-d 6qqh-d 6s46-d 6qqi-d 6otl-d 6qsa-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 (R57Q 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)	39.951, 39.951, 133.581
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 (R57Q mutant) Mass: 14855.712 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, 104 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.04 Å³/Da / Density % sol: 39.8 %
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: 0.9322 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2014 / Details: TOROIDAL MIRROR
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9322 Å / Relative weight: 1
Reflection	Resolution: 1.1→38.28 Å / Num. obs: 45101 / % possible obs: 100 % / Redundancy: 12.4 % / B_iso Wilson estimate: 14.5 Å² / CC_1/2: 1 / R_rim(I) all: 0.084 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.1→1.14 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4488 / CC_1/2: 0.596 / R_rim(I) all: 1.199 / % possible all: 100

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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: 1.1→38.28 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.973 / SU B: 1.169 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1702	2275	5.044 %
R_work	0.1443	42825	-
all	0.145	-	-
obs	-	45100	99.971 %

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: 13.784 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.201 Å²	0 Å²	0 Å²
2-	-	-0.201 Å²	0 Å²
3-	-	-	0.401 Å²

Refinement step

Cycle: LAST / Resolution: 1.1→38.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	941	0	34	100	1075

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.013	1116
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1059
X-RAY DIFFRACTION	r_angle_refined_deg	2.246	1.65	1539
X-RAY DIFFRACTION	r_angle_other_deg	1.541	1.581	2454
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.136	5	140
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.412	22.923	65
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.574	15	198
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.212	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	145
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	1285
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	259
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	208
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.207	0.2	1004
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	500
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	553
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.201	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.31	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.328	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.293	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.274	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.297	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	1.636	1.207	492
X-RAY DIFFRACTION	r_mcbond_other	1.576	1.203	491
X-RAY DIFFRACTION	r_mcangle_it	2.009	1.818	621
X-RAY DIFFRACTION	r_mcangle_other	2.045	1.825	622
X-RAY DIFFRACTION	r_scbond_it	3.839	1.423	624
X-RAY DIFFRACTION	r_scbond_other	3.847	1.424	621
X-RAY DIFFRACTION	r_scangle_it	4.193	2.03	906
X-RAY DIFFRACTION	r_scangle_other	4.191	2.029	907
X-RAY DIFFRACTION	r_lrange_it	3.598	13.982	1315
X-RAY DIFFRACTION	r_lrange_other	3.531	13.613	1293
X-RAY DIFFRACTION	r_rigid_bond_restr	4.052	3	2175

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 (%)
1.1-1.129	0.282	166	0.255	3113	X-RAY DIFFRACTION	99.9695
1.129-1.159	0.231	193	0.229	2975	X-RAY DIFFRACTION	100
1.159-1.193	0.241	188	0.205	2914	X-RAY DIFFRACTION	99.9034
1.193-1.23	0.237	145	0.19	2862	X-RAY DIFFRACTION	100
1.23-1.27	0.209	149	0.175	2768	X-RAY DIFFRACTION	100
1.27-1.315	0.208	142	0.164	2705	X-RAY DIFFRACTION	100
1.315-1.364	0.173	140	0.147	2588	X-RAY DIFFRACTION	99.817
1.364-1.42	0.156	114	0.123	2549	X-RAY DIFFRACTION	99.9625
1.42-1.483	0.163	144	0.115	2420	X-RAY DIFFRACTION	100
1.483-1.555	0.138	98	0.096	2304	X-RAY DIFFRACTION	100
1.555-1.639	0.144	110	0.094	2214	X-RAY DIFFRACTION	100
1.639-1.738	0.165	111	0.103	2114	X-RAY DIFFRACTION	100
1.738-1.858	0.14	120	0.108	1958	X-RAY DIFFRACTION	100
1.858-2.006	0.154	106	0.114	1848	X-RAY DIFFRACTION	100
2.006-2.197	0.142	96	0.121	1702	X-RAY DIFFRACTION	99.9444
2.197-2.456	0.17	67	0.13	1587	X-RAY DIFFRACTION	99.8792
2.456-2.834	0.168	62	0.149	1416	X-RAY DIFFRACTION	100
2.834-3.466	0.201	53	0.161	1205	X-RAY DIFFRACTION	100
3.466-4.881	0.118	46	0.138	977	X-RAY DIFFRACTION	100
4.881-38.28	0.198	25	0.228	606	X-RAY DIFFRACTION	100

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