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- PDB-2v0u: n- and c-terminal helices of oat lov2 (404-546) are involved in l... -

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Basic information

Entry
Database: PDB / ID: 2v0u
Titlen- and c-terminal helices of oat lov2 (404-546) are involved in light-induced signal transduction (cryo dark structure of lov2 (404-546))
ComponentsNPH1-1
KeywordsTRANSFERASE / LOV2 / KINASE / ATP-BINDING / AVENA SATIVA / SERINE/THREONINE-PROTEIN KINASE / LIGHT-INDUCED SIGNAL TRANSDUCTION / PHOTOTROPIN1 / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


blue light photoreceptor activity / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / metal ion binding
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 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesAVENA SATIVA (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHalavaty, A.S. / Moffat, K.
CitationJournal: Biochemistry / Year: 2007
Title: N- and C-Terminal Flanking Regions Modulate Light-Induced Signal Transduction in the Lov2 Domain of the Blue Light Sensor Phototropin 1 from Avena Sativa.
Authors: Halavaty, A.S. / Moffat, K.
History
DepositionMay 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NPH1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8628
Polymers16,8531
Non-polymers1,0097
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.549, 56.129, 66.778
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 / LOV2


Mass: 16853.008 Da / Num. of mol.: 1 / Fragment: LIGHT, OXYGEN, VOLTAGE DOMAIN, RESIDUES 404-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVENA SATIVA (oats) / Plasmid: PHIS-GB1-PARALLEL1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O49003
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST THREE N-TERMINAL RESIDUES DO NOT BELONG TO LOV2 SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.96 % / Description: NONE

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Details: BENT CONICAL SI-MIRROR (RH COATED)
RadiationMonochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 26704 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 36
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G28

1g28


Resolution: 1.4→24.34 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.874 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1340 5 %RANDOM
Rwork0.165 ---
obs0.167 25307 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→24.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 67 173 1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221331
X-RAY DIFFRACTIONr_bond_other_d0.0020.02928
X-RAY DIFFRACTIONr_angle_refined_deg1.2932.0171808
X-RAY DIFFRACTIONr_angle_other_deg0.88732270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6224.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15815239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9391511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_nbd_refined0.2460.2250
X-RAY DIFFRACTIONr_nbd_other0.1880.21030
X-RAY DIFFRACTIONr_nbtor_refined0.180.2668
X-RAY DIFFRACTIONr_nbtor_other0.0840.2676
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9391.51016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02221252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1093668
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9764.5548
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 106
Rwork0.207 1754
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66040.0516-1.65022.43840.44353.9334-0.0773-0.0077-0.13260.0014-0.01130.15870.1679-0.28550.08860.0087-0.02070.0053-0.08050.0146-0.00693.338-6.68611.257
21.4878-0.2738-0.65710.648-0.06340.7761-0.0188-0.11810.0170.01530.02430.00210.00470.0392-0.00550.0221-0.0011-0.0112-0.0950.0031-0.032116.5031.0166.986
31.0328-0.2901-0.37660.80070.07842.11740.00460.07160.0392-0.00980.0084-0.00520.0129-0.1065-0.0130.0270.0031-0.0179-0.0663-0.0125-0.04089.638-0.145-5.337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 414
2X-RAY DIFFRACTION2A415 - 516
3X-RAY DIFFRACTION3A517 - 546

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