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- PDB-6gpu: Crystal structure of miniSOG at 1.17A resolution -

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Basic information

Entry
Database: PDB / ID: 6gpu
TitleCrystal structure of miniSOG at 1.17A resolution
ComponentsPhototropin-2
KeywordsFLAVOPROTEIN / Singlet oxygen generator / fluorescent protein / FMN
Function / homology
Function and homology information


chloroplast relocation / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation ...chloroplast relocation / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain ...PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / Phototropin-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsLafaye, C. / Signor, L. / Aumonier, S. / Shu, X. / Gotthard, G. / Royant, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-JSV5-0009 France
CitationJournal: 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
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0216
Polymers13,3241
Non-polymers6975
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-30 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.020, 40.020, 134.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phototropin-2 / Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / NPH1- ...Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / NPH1-like protein 1


Mass: 13324.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EFIPNPLLG / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P93025, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 156 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.04 %
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, 0 or 15 mM CoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 23, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.17→80 Å / Num. obs: 37913 / % possible obs: 99.8 % / Redundancy: 8.2 % / Biso Wilson estimate: 16.235 Å2 / CC1/2: 1 / Rrim(I) all: 0.062 / Net I/σ(I): 22.1
Reflection shellResolution: 1.17→1.2 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2747 / CC1/2: 0.704 / Rrim(I) all: 1.205 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
REFMAC5.8.0218refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eep

4eep


Resolution: 1.17→38.35 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.289 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 1850 4.9 %RANDOM
Rwork0.13265 ---
obs0.13414 36063 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.17→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 42 151 1125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021141
X-RAY DIFFRACTIONr_bond_other_d0.0010.021099
X-RAY DIFFRACTIONr_angle_refined_deg1.72.0191575
X-RAY DIFFRACTIONr_angle_other_deg0.83432581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96224.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17615223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.151511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.451.264504
X-RAY DIFFRACTIONr_mcbond_other1.4111.254502
X-RAY DIFFRACTIONr_mcangle_it1.881.903637
X-RAY DIFFRACTIONr_mcangle_other1.8821.91638
X-RAY DIFFRACTIONr_scbond_it1.8871.485637
X-RAY DIFFRACTIONr_scbond_other1.891.485637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.342.133917
X-RAY DIFFRACTIONr_long_range_B_refined3.79215.9051427
X-RAY DIFFRACTIONr_long_range_B_other3.79115.9081428
X-RAY DIFFRACTIONr_rigid_bond_restr1.79732240
X-RAY DIFFRACTIONr_sphericity_free23.7595
X-RAY DIFFRACTIONr_sphericity_bonded8.42652257
LS refinement shellResolution: 1.17→1.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 140 -
Rwork0.234 2601 -
obs--99.85 %

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