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- PDB-4wf0: Crystal Structure of iLID - an Improved Light-Inducible Dimer -

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Basic information

Entry
Database: PDB / ID: 4wf0
TitleCrystal Structure of iLID - an Improved Light-Inducible Dimer
ComponentsNPH1-1
KeywordsFLAVOPROTEIN / light-inducible dimer
Function / homology
Function and homology information


blue light photoreceptor activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / ATP binding / metal ion binding
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 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesAvena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHallett, R. / Williams, T. / Kuhlman, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093208 United States
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins.
Authors: Guntas, G. / Hallett, R.A. / Zimmerman, S.P. / Williams, T. / Yumerefendi, H. / Bear, J.E. / Kuhlman, B.
#1: Journal: Chem. Biol. / Year: 2012
Title: Designing photoswitchable peptides using the AsLOV2 domain.
Authors: Lungu, O.I. / Hallett, R.A. / Choi, E.J. / Aiken, M.J. / Hahn, K.M. / Kuhlman, B.
History
DepositionSep 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NPH1-1
B: NPH1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5235
Polymers36,5752
Non-polymers9483
Water4,612256
1
A: NPH1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7442
Polymers18,2881
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NPH1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7793
Polymers18,2881
Non-polymers4922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.156, 70.339, 80.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NPH1-1


Mass: 18287.562 Da / Num. of mol.: 2 / Fragment: UNP residues 405-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-1 / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O49003
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Fragment: Flavin mononucleotide cofactor / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Grown in dark for 3 days. Conditions: 100mM TRIS:HCl pH 8.5, 800mM Lithium Chloride, 32% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Jan 31, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→80.38 Å / Num. obs: 26353 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 25.37 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.63

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v0u

2v0u


Resolution: 1.95→31.078 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1331 5.08 %
Rwork0.231 --
obs0.2317 26208 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→31.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 63 256 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132510
X-RAY DIFFRACTIONf_angle_d1.2573414
X-RAY DIFFRACTIONf_dihedral_angle_d17.326954
X-RAY DIFFRACTIONf_chiral_restr0.056370
X-RAY DIFFRACTIONf_plane_restr0.006442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01970.4341300.37882440X-RAY DIFFRACTION100
2.0197-2.10050.3371100.32522472X-RAY DIFFRACTION100
2.1005-2.19610.31191460.29282439X-RAY DIFFRACTION100
2.1961-2.31190.26341270.25782467X-RAY DIFFRACTION100
2.3119-2.45670.24741310.22772455X-RAY DIFFRACTION100
2.4567-2.64620.25731500.21792463X-RAY DIFFRACTION100
2.6462-2.91240.18761210.20622498X-RAY DIFFRACTION100
2.9124-3.33340.22761460.19192506X-RAY DIFFRACTION100
3.3334-4.19810.21821410.18922515X-RAY DIFFRACTION100
4.1981-31.08190.21981290.2352622X-RAY DIFFRACTION98

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