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

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Basic information

Entry
Database: PDB / ID: 7qf3
TitleStructure of the R57Q mutant of miniSOG expressed in E. coli in regular LB medium
ComponentsminiSOG (R57Q mutant)
KeywordsFLAVOPROTEIN / LOV DOMAIN / RIBOFLAVIN / PHOTOSENSITIZING PROTEIN / FLUORESCENT PROTEIN
Function / homology: / FLAVIN MONONUCLEOTIDE
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLafaye, C. / Aumonier, S. / von Stetten, D. / Noirclerc-Savoye, N. / Gotthard, G. / Royant, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-JSV5-0009 France
Citation
#1: Journal: Sci Rep / Year: 2019
Title: Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein.
Authors: Torra, J. / Lafaye, C. / Signor, L. / Aumonier, S. / Flors, C. / Shu, X. / Nonell, S. / Gotthard, G. / Royant, A.
History
DepositionDec 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: miniSOG (R57Q mutant)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4315
Polymers14,8561
Non-polymers5754
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number96
Space group name H-MP43212

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Components

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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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / 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 interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 1.1→38.28 Å / Num. obs: 45101 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.084 / Net I/σ(I): 15.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4488 / CC1/2: 0.596 / Rrim(I) all: 1.199 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GPU

6gpu


Resolution: 1.1→38.28 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflection
Rfree0.1702 2275 5.044 %
Rwork0.1443 42825 -
all0.145 --
obs-45100 99.971 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.201 Å20 Å20 Å2
2---0.201 Å20 Å2
3---0.401 Å2
Refinement stepCycle: LAST / Resolution: 1.1→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 34 100 1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131116
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151059
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.651539
X-RAY DIFFRACTIONr_angle_other_deg1.5411.5812454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1365140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41222.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57415198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.212158
X-RAY DIFFRACTIONr_chiral_restr0.1320.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021285
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02259
X-RAY DIFFRACTIONr_nbd_refined0.2320.2208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.21004
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2500
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.310.21
X-RAY DIFFRACTIONr_metal_ion_refined0.3280.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2930.217
X-RAY DIFFRACTIONr_nbd_other0.2740.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2970.28
X-RAY DIFFRACTIONr_mcbond_it1.6361.207492
X-RAY DIFFRACTIONr_mcbond_other1.5761.203491
X-RAY DIFFRACTIONr_mcangle_it2.0091.818621
X-RAY DIFFRACTIONr_mcangle_other2.0451.825622
X-RAY DIFFRACTIONr_scbond_it3.8391.423624
X-RAY DIFFRACTIONr_scbond_other3.8471.424621
X-RAY DIFFRACTIONr_scangle_it4.1932.03906
X-RAY DIFFRACTIONr_scangle_other4.1912.029907
X-RAY DIFFRACTIONr_lrange_it3.59813.9821315
X-RAY DIFFRACTIONr_lrange_other3.53113.6131293
X-RAY DIFFRACTIONr_rigid_bond_restr4.05232175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.1290.2821660.2553113X-RAY DIFFRACTION99.9695
1.129-1.1590.2311930.2292975X-RAY DIFFRACTION100
1.159-1.1930.2411880.2052914X-RAY DIFFRACTION99.9034
1.193-1.230.2371450.192862X-RAY DIFFRACTION100
1.23-1.270.2091490.1752768X-RAY DIFFRACTION100
1.27-1.3150.2081420.1642705X-RAY DIFFRACTION100
1.315-1.3640.1731400.1472588X-RAY DIFFRACTION99.817
1.364-1.420.1561140.1232549X-RAY DIFFRACTION99.9625
1.42-1.4830.1631440.1152420X-RAY DIFFRACTION100
1.483-1.5550.138980.0962304X-RAY DIFFRACTION100
1.555-1.6390.1441100.0942214X-RAY DIFFRACTION100
1.639-1.7380.1651110.1032114X-RAY DIFFRACTION100
1.738-1.8580.141200.1081958X-RAY DIFFRACTION100
1.858-2.0060.1541060.1141848X-RAY DIFFRACTION100
2.006-2.1970.142960.1211702X-RAY DIFFRACTION99.9444
2.197-2.4560.17670.131587X-RAY DIFFRACTION99.8792
2.456-2.8340.168620.1491416X-RAY DIFFRACTION100
2.834-3.4660.201530.1611205X-RAY DIFFRACTION100
3.466-4.8810.118460.138977X-RAY DIFFRACTION100
4.881-38.280.198250.228606X-RAY DIFFRACTION100

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