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- PDB-4eeu: Crystal structure of phiLOV2.1 -

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Basic information

Entry
Database: PDB / ID: 4eeu
TitleCrystal structure of phiLOV2.1
ComponentsPhototropin-2
KeywordsSIGNALING PROTEIN / FLAVOPROTEIN / LOV / Blue light photoreceptor
Function / homology
Function and homology information


chloroplast relocation / negative regulation of anion channel activity by blue light / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity ...chloroplast relocation / negative regulation of anion channel activity by blue light / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
PAS-associated, C-terminal / PAC domain profile. / PAS domain / 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-associated, C-terminal / PAC domain profile. / PAS domain / 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: 1.4068 Å
AuthorsHitomi, K. / Christie, J.M. / Arvai, A.S. / Hartfield, K.A. / Pratt, A.J. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Tuning of the Fluorescent Protein iLOV for Improved Photostability.
Authors: Christie, J.M. / Hitomi, K. / Arvai, A.S. / Hartfield, K.A. / Mettlen, M. / Pratt, A.J. / Tainer, J.A. / Getzoff, E.D.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jul 11, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9842
Polymers13,5271
Non-polymers4561
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.967, 40.967, 130.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phototropin-2 / / Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / AtKin7 ...Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / AtKin7 / NPH1-like protein 1


Mass: 13527.299 Da / Num. of mol.: 1 / Fragment: LOV DOMAIN (UNP Residues 385-496)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 / Production host: Escherichia coli (E. coli)
References: UniProt: P93025, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 39.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 25% MPEG 2K, 0.2 M imidazole malate, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11611 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11611 Å / Relative weight: 1
ReflectionResolution: 1.4→26.5 Å / Num. obs: 21959

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EES

4ees


Resolution: 1.4068→26.478 Å / SU ML: 0.17 / σ(F): 0.12 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 1102 5.02 %
Rwork0.2012 --
obs0.2018 21959 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.077 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6102 Å20 Å2-0 Å2
2--2.6102 Å2-0 Å2
3----5.2205 Å2
Refinement stepCycle: LAST / Resolution: 1.4068→26.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 31 98 1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009937
X-RAY DIFFRACTIONf_angle_d1.2341270
X-RAY DIFFRACTIONf_dihedral_angle_d16.581353
X-RAY DIFFRACTIONf_chiral_restr0.078136
X-RAY DIFFRACTIONf_plane_restr0.007161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4068-1.47080.23131320.19662460X-RAY DIFFRACTION95
1.4708-1.54830.22591290.18342457X-RAY DIFFRACTION95
1.5483-1.64530.19221350.17822585X-RAY DIFFRACTION98
1.6453-1.77230.19771380.18122584X-RAY DIFFRACTION98
1.7723-1.95070.22891360.18612582X-RAY DIFFRACTION97
1.9507-2.23280.2021400.18152638X-RAY DIFFRACTION99
2.2328-2.81260.19491420.20282690X-RAY DIFFRACTION99
2.8126-26.48260.21041500.20482861X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.1271 Å / Origin y: 4.7287 Å / Origin z: -19.6434 Å
111213212223313233
T0.1265 Å2-0 Å20.0052 Å2-0.1607 Å2-0.0132 Å2--0.1481 Å2
L1.4096 °2-0.5892 °20.53 °2-2.075 °20.3824 °2--2.4462 °2
S-0.0615 Å °-0.1043 Å °0.0428 Å °0.1096 Å °0.1606 Å °-0.0268 Å °-0.0571 Å °0.19 Å °-0.0638 Å °
Refinement TLS groupSelection details: all

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