PDB-7qf4: Structure of the R57Q mutant of miniSOG expressed in E. coli in L...

ID or keywords:

Entry

Database: PDB / ID: 7qf4

Title

Structure of the R57Q mutant of miniSOG expressed in E. coli in LB medium enriched with riboflavin

Components

miniSOG (R57Q mutant)

Keywords

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

Function / homology

: / RIBOFLAVIN

Function and homology information

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.17 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	7qf4.cif.gz	69 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qf4_validation.pdf.gz	818.3 KB	Display	wwPDB validaton report
Full document	7qf4_full_validation.pdf.gz	819.6 KB	Display
Data in XML	7qf4_validation.xml.gz	8.2 KB	Display
Data in CIF	7qf4_validation.cif.gz	10.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/7qf4 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qf4	HTTPS FTP

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Related structure data

Related structure data	7qf2C 7qf3C 7qf5C 6gpuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7qf5-d 7qf2-d 7qf3-d 6s46-d 6owu-2 6otl-d 5wwx-d 3oz1-4 6lmr-d 4ipc-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

15.3 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)	39.930, 39.930, 134.650
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-357- HOH

#1: Protein	miniSOG (R57Q mutant) Mass: 14869.737 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)
#2: Chemical	ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₀N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O
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: 40.2 %
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: 0.984 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2015 / Details: TOROIDAL MIRROR
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.984 Å / Relative weight: 1
Reflection	Resolution: 1.17→38.29 Å / Num. obs: 37774 / % possible obs: 99.7 % / Redundancy: 8.1 % / B_iso Wilson estimate: 15.8 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.06 / Net I/σ(I): 17.9
Reflection shell	Resolution: 1.17→1.2 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2702 / CC_1/2: 0.646 / R_rim(I) all: 1 / % possible all: 99.1

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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: 1.17→38.282 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.967 / SU B: 1.397 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1821	1800	4.765 %
R_work	0.1464	35974	-
all	0.148	-	-
obs	-	37774	99.633 %

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: 13.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.224 Å²	0 Å²	0 Å²
2-	-	-0.224 Å²	0 Å²
3-	-	-	0.448 Å²

Refinement step

Cycle: LAST / Resolution: 1.17→38.282 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	942	0	29	93	1064

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.013	1077
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1040
X-RAY DIFFRACTION	r_angle_refined_deg	2.167	1.649	1480
X-RAY DIFFRACTION	r_angle_other_deg	1.53	1.581	2407
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.949	5	138
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.341	22.813	64
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.094	15	196
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.366	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	142
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	1243
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	255
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	192
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	951
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	501
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	525
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	48
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.151	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.23	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.16	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	1.435	1.175	490
X-RAY DIFFRACTION	r_mcbond_other	1.291	1.166	489
X-RAY DIFFRACTION	r_mcangle_it	1.628	1.765	618
X-RAY DIFFRACTION	r_mcangle_other	1.695	1.774	619
X-RAY DIFFRACTION	r_scbond_it	2.665	1.476	587
X-RAY DIFFRACTION	r_scbond_other	2.663	1.475	588
X-RAY DIFFRACTION	r_scangle_it	3.067	2.091	851
X-RAY DIFFRACTION	r_scangle_other	3.065	2.204	852
X-RAY DIFFRACTION	r_lrange_it	3.167	14.045	1218
X-RAY DIFFRACTION	r_lrange_other	3.008	20.205	1201
X-RAY DIFFRACTION	r_rigid_bond_restr	4.287	3	2116

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
1.17-1.2	0.257	132	0.252	2567	0.252	2724	0.834	0.841	99.0822	0.23
1.2-1.233	0.242	127	0.219	2553	0.22	2682	0.882	0.889	99.9254	0.193
1.233-1.269	0.253	127	0.215	2446	0.216	2574	0.862	0.897	99.9612	0.186
1.269-1.308	0.229	106	0.2	2440	0.202	2546	0.895	0.904	100	0.172
1.308-1.351	0.211	111	0.177	2316	0.179	2460	0.924	0.935	98.6585	0.148
1.351-1.398	0.204	128	0.143	2244	0.147	2377	0.937	0.954	99.7896	0.117
1.398-1.451	0.162	102	0.134	2205	0.135	2307	0.957	0.962	100	0.109
1.451-1.51	0.182	102	0.128	2117	0.131	2219	0.954	0.966	100	0.104
1.51-1.577	0.168	96	0.114	2035	0.116	2131	0.96	0.975	100	0.093
1.577-1.654	0.169	98	0.115	1947	0.117	2067	0.962	0.973	98.9357	0.096
1.654-1.743	0.172	116	0.11	1831	0.113	1947	0.967	0.977	100	0.094
1.743-1.849	0.186	95	0.117	1758	0.12	1853	0.961	0.976	100	0.101
1.849-1.976	0.151	73	0.124	1679	0.125	1752	0.974	0.977	100	0.11
1.976-2.134	0.152	72	0.123	1566	0.124	1638	0.974	0.98	100	0.115
2.134-2.337	0.157	72	0.127	1442	0.128	1533	0.973	0.977	98.7606	0.122
2.337-2.611	0.163	77	0.138	1298	0.14	1377	0.973	0.977	99.8548	0.135
2.611-3.013	0.21	52	0.146	1189	0.148	1242	0.951	0.972	99.9195	0.147
3.013-3.684	0.206	46	0.16	1027	0.161	1073	0.955	0.971	100	0.172
3.684-5.187	0.149	37	0.14	815	0.141	863	0.982	0.982	98.7254	0.159
5.187-38.282	0.215	31	0.215	499	0.215	536	0.967	0.964	98.8806	0.25

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