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- PDB-7yx0: Crystal structure of the full-length short LOV protein SBW25-LOV ... -

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Basic information

Entry
Database: PDB / ID: 7yx0
TitleCrystal structure of the full-length short LOV protein SBW25-LOV from Pseudomonas fluorescens (light state)
ComponentsPutative regulatory protein
KeywordsSIGNALING PROTEIN / LOV domain / short LOV / PAS domain / Photocycle / Dimerization / Signaling blue light photoreceptor
Function / homology
Function and homology information


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 repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / Flavin mononucleotide (semi-quinone intermediate) / Regulatory protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsArinkin, V. / Batra-Safferling, R. / Granzin, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Conserved Signal Transduction Mechanisms and Dark Recovery Kinetic Tuning in the Pseudomonadaceae Short Light, Oxygen, Voltage (LOV) Protein Family.
Authors: Arinkin, V. / Granzin, J. / Jaeger, K.E. / Willbold, D. / Krauss, U. / Batra-Safferling, R.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative regulatory protein
C: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2128
Polymers39,3002
Non-polymers1,9116
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.255, 42.438, 51.744
Angle α, β, γ (deg.)95.269, 95.707, 109.017
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Putative regulatory protein


Mass: 19650.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PFLU_5153 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3K1W0

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Non-polymers , 5 types, 124 molecules

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


Mass: 456.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-JGC / Flavin mononucleotide (semi-quinone intermediate) / [(2R,3S,4S)-5-[(4aR)-7,8-dimethyl-2,4-bis(oxidanylidene)-4a,5-dihydrobenzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.89 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 3350, 0.1 M MES / PH range: 6.0 - 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2015
RadiationMonochromator: Si (111), Pt coated mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.6→39.77 Å / Num. obs: 36845 / % possible obs: 97 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.059 / Rrim(I) all: 0.11 / Net I/σ(I): 5
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.705 / Num. unique obs: 1827 / CC1/2: 0.761 / Rpim(I) all: 0.444 / Rrim(I) all: 0.836

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.17.1_3660refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SW1

3sw1


Resolution: 1.6→33.95 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.6339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2385 1740 4.72 %
Rwork0.1882 35087 -
obs0.1906 36827 96.92 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 129 118 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582753
X-RAY DIFFRACTIONf_angle_d0.78833750
X-RAY DIFFRACTIONf_chiral_restr0.0483407
X-RAY DIFFRACTIONf_plane_restr0.005483
X-RAY DIFFRACTIONf_dihedral_angle_d19.02411041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.30121500.2222919X-RAY DIFFRACTION95.31
1.65-1.70.30751510.22442847X-RAY DIFFRACTION95.84
1.7-1.760.30491530.21252897X-RAY DIFFRACTION96.03
1.76-1.830.26181330.20292944X-RAY DIFFRACTION96.34
1.83-1.910.2481350.19422909X-RAY DIFFRACTION96.57
1.91-2.020.27121330.18262951X-RAY DIFFRACTION97.2
2.02-2.140.23951540.18022913X-RAY DIFFRACTION97.4
2.14-2.310.25531470.18172909X-RAY DIFFRACTION97.08
2.31-2.540.27181460.19452917X-RAY DIFFRACTION96.96
2.54-2.910.24271390.22954X-RAY DIFFRACTION97.82
2.91-3.660.22281440.18572972X-RAY DIFFRACTION98.3
3.66-33.950.20491550.17632955X-RAY DIFFRACTION98.23

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