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- PDB-4nxf: Crystal structure of iLOV-I486(2LT) at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 4nxf
TitleCrystal structure of iLOV-I486(2LT) at pH 8.0
ComponentsPhototropin-2
KeywordsFLAVOPROTEIN / FLUORESCENT PROTEIN / FMN binding
Function / homology
Function and homology information


chloroplast relocation / phototropism / stomatal movement / blue light photoreceptor activity / response to blue light / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation ...chloroplast relocation / phototropism / stomatal movement / blue light photoreceptor activity / response to blue light / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation / 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: 1.766 Å
AuthorsWang, J. / Liu, X. / Li, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Significant expansion of fluorescent protein sensing ability through the genetic incorporation of superior photo-induced electron-transfer quenchers.
Authors: Liu, X. / Jiang, L. / Li, J. / Wang, L. / Yu, Y. / Zhou, Q. / Lv, X. / Gong, W. / Lu, Y. / Wang, J.
History
DepositionDec 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: 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
A: Phototropin-2
B: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8524
Polymers27,9392
Non-polymers9132
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-19 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.233, 64.897, 49.362
Angle α, β, γ (deg.)90.00, 102.59, 90.00
Int Tables number4
Space group name H-MP1211

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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: 13969.408 Da / Num. of mol.: 2 / Fragment: LOV DOMAIN, UNP Residues 388-496 / Mutation: S394T, S409G, I452T, F470L, M475V, I486Y
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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES C426A IS MUTAGENESIS ACCORDING TO DATABASE P93025.

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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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: protein sample (20-30 mg/ml) in 20mM Tris, pH 8.0, 50mM NaCl, equal volume of reservoir solution (0.2M Ammonium acetate, 0.1M Tris pH 8.0, 16% w/v Polyethylene glycol 10000), VAPOR ...Details: protein sample (20-30 mg/ml) in 20mM Tris, pH 8.0, 50mM NaCl, equal volume of reservoir solution (0.2M Ammonium acetate, 0.1M Tris pH 8.0, 16% w/v Polyethylene glycol 10000), VAPOR DIFFUSION, SITTING DROP, temperature 289.0 K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.766→50 Å / Num. all: 22542 / Num. obs: 21167 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.766→1.8 Å / Redundancy: 3.6 % / Num. unique all: 1066 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EES

4ees


Resolution: 1.766→24.203 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8606 / SU ML: 0.16 / σ(F): 1.43 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1053 5.07 %RANDOM
Rwork0.1958 ---
all0.1989 22572 --
obs0.1974 20782 92.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.74 Å2 / Biso mean: 24.1841 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: LAST / Resolution: 1.766→24.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 62 108 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081832
X-RAY DIFFRACTIONf_angle_d1.2382489
X-RAY DIFFRACTIONf_dihedral_angle_d18.662695
X-RAY DIFFRACTIONf_chiral_restr0.086260
X-RAY DIFFRACTIONf_plane_restr0.006319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7659-1.84620.2321280.2026224084
1.8462-1.94350.25221160.1832264399
1.9435-2.06520.23371430.1793266199
2.0652-2.22450.20131270.1783264099
2.2245-2.44820.23851400.1841263098
2.4482-2.8020.23171490.1945259597
2.802-3.52850.21991310.2089237989
3.5285-24.20530.22191190.2095194172
Refinement TLS params.Method: refined / Origin x: -3.5914 Å / Origin y: -2.4953 Å / Origin z: 60.3517 Å
111213212223313233
T0.1315 Å20.0021 Å20.0115 Å2-0.12 Å2-0.0119 Å2--0.1587 Å2
L0.6643 °20.012 °20.4849 °2-0.6375 °2-0.1731 °2--1.7441 °2
S0.0002 Å °0.0068 Å °-0.0411 Å °-0.0075 Å °-0.0192 Å °0.0145 Å °0.0202 Å °0.0409 Å °0.0077 Å °
Refinement TLS groupSelection details: ALL

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