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- PDB-8il9: Crystal structure of the LOV1 Q122N mutant of Klebsormidium niten... -

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Basic information

Entry
Database: PDB / ID: 8il9
TitleCrystal structure of the LOV1 Q122N mutant of Klebsormidium nitens phototropin
ComponentsPhototropin
KeywordsFLAVOPROTEIN / blue light photoreceptor
Function / homology
Function and homology information


blue light photoreceptor activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding / nucleus / 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
FLAVIN MONONUCLEOTIDE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesKlebsormidium nitens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsGautam, A.K. / Sharma, S. / Gourinath, S. / Kateriya, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: To Be Published
Title: Crystal structure of LOV1 Q122N mutant of phototropin from klebsormidium nitens
Authors: Gautam, A.K. / Sharma, S. / Gourinath, S. / kateria, S.
History
DepositionMar 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phototropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4532
Polymers16,9961
Non-polymers4561
Water1,874104
1
A: Phototropin
hetero molecules

A: Phototropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9054
Polymers33,9932
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4060 Å2
ΔGint-29 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.878, 53.878, 137.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phototropin


Mass: 16996.293 Da / Num. of mol.: 1 / Mutation: Q122N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsormidium nitens (plant) / Gene: KFL_000480260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y1HNG4
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: Nickel chloride hexahydrate, Tris pH 8.5, lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918402 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918402 Å / Relative weight: 1
ReflectionResolution: 2.156→38.098 Å / Num. obs: 13135 / % possible obs: 98.6 % / Redundancy: 24.4 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Net I/σ(I): 21.5
Reflection shellResolution: 2.156→5.847 Å / Num. unique obs: 11392 / CC1/2: 1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.162 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2224 612 5.372 %
Rwork0.1845 10780 -
all0.187 --
obs-10780 98.462 %
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: 45.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.416 Å2-0 Å2-0 Å2
2--0.416 Å2-0 Å2
3----0.831 Å2
Refinement stepCycle: LAST / Resolution: 2.16→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 31 104 1031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.012953
X-RAY DIFFRACTIONr_bond_other_d0.0010.016877
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6531294
X-RAY DIFFRACTIONr_angle_other_deg0.5611.5652019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.22655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29610151
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.0031041
X-RAY DIFFRACTIONr_chiral_restr0.0880.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
X-RAY DIFFRACTIONr_nbd_refined0.230.2186
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.2806
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2481
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.218
X-RAY DIFFRACTIONr_nbd_other0.1610.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0240.22
X-RAY DIFFRACTIONr_mcbond_it4.8774.952472
X-RAY DIFFRACTIONr_mcbond_other4.8114.956472
X-RAY DIFFRACTIONr_mcangle_it6.4228.849590
X-RAY DIFFRACTIONr_mcangle_other6.4228.863591
X-RAY DIFFRACTIONr_scbond_it6.4495.354481
X-RAY DIFFRACTIONr_scbond_other6.4485.355478
X-RAY DIFFRACTIONr_scangle_it9.4989.607704
X-RAY DIFFRACTIONr_scangle_other9.4919.602705
X-RAY DIFFRACTIONr_lrange_it10.40561.9681164
X-RAY DIFFRACTIONr_lrange_other10.43857.1841140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.2730.299280.264644X-RAY DIFFRACTION83.2714
2.273-2.3380.342400.209748X-RAY DIFFRACTION100
2.338-2.410.244330.219732X-RAY DIFFRACTION100
2.41-2.4890.224420.196693X-RAY DIFFRACTION100
2.489-2.5750.267410.208692X-RAY DIFFRACTION100
2.575-2.6720.256390.184657X-RAY DIFFRACTION100
2.672-2.7810.207320.183638X-RAY DIFFRACTION100
2.781-2.9040.241410.191611X-RAY DIFFRACTION100
3.045-3.2080.327370.218559X-RAY DIFFRACTION100
3.208-3.4010.231300.201531X-RAY DIFFRACTION100
3.634-3.9220.175270.167473X-RAY DIFFRACTION100
3.922-4.2920.221400.148428X-RAY DIFFRACTION100
4.292-4.7910.141190.138413X-RAY DIFFRACTION100
4.791-5.5180.179170.139372X-RAY DIFFRACTION100
5.518-6.7230.259170.212321X-RAY DIFFRACTION100
6.723-9.3630.249100.199260X-RAY DIFFRACTION100

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