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- PDB-2v1b: N- and C-terminal helices of oat LOV2 (404-546) are involved in l... -

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Basic information

Entry
Database: PDB / ID: 2v1b
TitleN- and C-terminal helices of oat LOV2 (404-546) are involved in light-induced signal transduction (room temperature (293K) light 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: 1.55 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 22, 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 1.2Oct 9, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / reflns ...pdbx_database_status / reflns / reflns_shell / struct_conn
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs ..._pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NPH1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2153
Polymers16,6671
Non-polymers5482
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.919, 57.169, 67.228
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: 16666.840 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPHE403 (VECTOR RESIDUE) DOES 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: 2.16 Å3/Da / Density % sol: 43.01 % / Description: NONE

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002
DetectorType: ADSC CCD / 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: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 19930 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 96

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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 2V0U

2v0u


Resolution: 1.55→16.12 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.029 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1012 5.1 %RANDOM
Rwork0.164 ---
obs0.166 18897 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.55→16.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 37 140 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221299
X-RAY DIFFRACTIONr_bond_other_d0.0010.02892
X-RAY DIFFRACTIONr_angle_refined_deg1.6342.0021774
X-RAY DIFFRACTIONr_angle_other_deg0.96632186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40524.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25115237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1751511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined0.2110.2246
X-RAY DIFFRACTIONr_nbd_other0.1980.2946
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2639
X-RAY DIFFRACTIONr_nbtor_other0.0880.2674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3411.51010
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41521243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9273641
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0644.5522
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: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 83
Rwork0.235 1332
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)
16.88722.9965-2.34579.4171-4.257211.5952-0.05780.2652-0.0426-0.18280.38840.63920.3169-0.8178-0.3306-0.0381-0.0417-0.0325-0.19730.04660.01722.645-5.9510.109
21.9843-0.2326-0.93421.0582-0.20521.64470.022-0.1672-0.00690.0551-0.0354-0.0269-0.06920.1180.01340.0197-0.0126-0.0176-0.21070.0063-0.040116.5691.1337.044
31.1801-0.00360.43691.3956-0.65083.6250.03390.15810.033-0.02470.03460.0269-0.0969-0.226-0.06850.03290.0172-0.0364-0.2275-0.0211-0.0549.471-0.146-5.239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A403 - 414
2X-RAY DIFFRACTION2A415 - 516
3X-RAY DIFFRACTION3A517 - 546

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