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- PDB-7ph0: Structure of light-adapted AsLOV2 Q513L -

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Basic information

Entry
Database: PDB / ID: 7ph0
TitleStructure of light-adapted AsLOV2 Q513L
ComponentsNPH1-1
KeywordsSIGNALING PROTEIN / flavin / light-oxygen-voltage / optogenetics / photoreceptor / phototropin
Function / homology
Function and homology information


blue light photoreceptor activity / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm
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 / PAS repeat profile. / PAS domain / PAS domain superfamily / Serine/threonine-protein kinase, active site ...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 / 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
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesAvena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.979 Å
AuthorsGelfert, R. / Weyand, M. / Moeglich, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)MO2192/8-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine.
Authors: Dietler, J. / Gelfert, R. / Kaiser, J. / Borin, V. / Renzl, C. / Pilsl, S. / Ranzani, A.T. / Garcia de Fuentes, A. / Gleichmann, T. / Diensthuber, R.P. / Weyand, M. / Mayer, G. / Schapiro, I. / Moglich, A.
History
DepositionAug 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: NPH1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7899
Polymers16,8381
Non-polymers9518
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-11 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.280, 56.040, 66.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein NPH1-1


Mass: 16838.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CmpX13 / References: UniProt: O49003

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Non-polymers , 6 types, 225 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2020
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.979→42.925 Å / Num. obs: 76537 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 13.6
Reflection shellResolution: 0.98→1.04 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 12003 / CC1/2: 0.28 / % possible all: 7.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V0U

2v0u


Resolution: 0.979→42.925 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.981 / WRfactor Rfree: 0.134 / WRfactor Rwork: 0.104 / SU B: 0.95 / SU ML: 0.021 / Average fsc free: 0.912 / Average fsc work: 0.917 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.024
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1357 3827 5 %
Rwork0.1121 72710 -
all0.113 --
obs-76537 99.633 %
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: 15.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.415 Å2-0 Å2
3----0.306 Å2
Refinement stepCycle: LAST / Resolution: 0.979→42.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 62 217 1464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171947
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.6662792
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5924539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9515253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.68322.5128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1641519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02473
X-RAY DIFFRACTIONr_nbd_refined0.3960.2383
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.21447
X-RAY DIFFRACTIONr_nbtor_refined0.180.2687
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.243
X-RAY DIFFRACTIONr_nbd_other0.2170.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.23
X-RAY DIFFRACTIONr_mcbond_it1.3981.243914
X-RAY DIFFRACTIONr_mcbond_other1.3991.237911
X-RAY DIFFRACTIONr_mcangle_it1.8741.861161
X-RAY DIFFRACTIONr_mcangle_other1.8731.861162
X-RAY DIFFRACTIONr_scbond_it2.3921.5431120
X-RAY DIFFRACTIONr_scbond_other2.3921.5461121
X-RAY DIFFRACTIONr_scangle_it2.7922.211606
X-RAY DIFFRACTIONr_scangle_other2.7912.2131607
X-RAY DIFFRACTIONr_lrange_it3.36915.242180
X-RAY DIFFRACTIONr_lrange_other3.2614.5362130
X-RAY DIFFRACTIONr_rigid_bond_restr2.66633966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
0.979-1.0050.3842660.38250640.38255760.580.60195.58820.387
1.005-1.0320.3012730.32351890.32254700.6850.69599.85370.322
1.032-1.0620.2652670.2650570.26153290.840.84199.90620.246
1.062-1.0950.2372570.21448980.21551590.8970.90399.92250.189
1.095-1.1310.1882520.17247730.17350280.9350.93599.94030.142
1.131-1.170.152430.14446230.14448680.9560.95799.95890.115
1.17-1.2150.1462350.12144780.12347130.9690.9691000.095
1.215-1.2640.1262260.10442890.10545150.9750.9771000.08
1.264-1.320.1212170.08941170.09143350.9770.98299.97690.069
1.32-1.3850.1082080.07639500.07841600.9830.98799.95190.06
1.385-1.4590.1161980.06837660.07139660.9840.98999.94960.056
1.459-1.5480.1051880.06335780.06537660.9860.9911000.054
1.548-1.6550.0971770.06433600.06635380.9880.99299.97170.058
1.655-1.7870.1171660.07131420.07333080.9830.991000.067
1.787-1.9570.1191530.07829230.0830760.9850.991000.079
1.957-2.1880.1111390.0826240.08227630.9870.9911000.087
2.188-2.5250.1061230.08823480.08924740.9860.98999.87870.103
2.525-3.090.1291050.10620030.10721080.9830.9851000.127
3.09-4.3580.118840.10515920.10516780.9850.98899.88080.137
4.358-42.9250.194500.2049360.2049890.9670.9799.69670.307

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