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- PDB-2v0w: N- and C-terminal helices of oat LOV2 (404-546) are involved in l... -

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Basic information

Entry
Database: PDB / ID: 2v0w
TitleN- and C-terminal helices of oat LOV2 (404-546) are involved in light- induced signal transduction (cryo-trapped light structure of LOV2 (404-546))
ComponentsNPH1-1
KeywordsTRANSFERASE / LOV2 / KINASE / ATP-BINDING / AVENA SATIVA / SERINE/THREONINE-PROTEIN KINASE / PHOTOTROPIN1 / LIGHT-INDUCED SIGNAL TRANSDUCTION / 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: 1.7 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 20, 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 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_validate_polymer_linkage / reflns / reflns_shell / struct_conn
Item: _pdbx_database_status.status_code_sf / _pdbx_validate_polymer_linkage.dist ..._pdbx_database_status.status_code_sf / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2 / _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)17,5865
Polymers16,8531
Non-polymers7334
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.565, 56.021, 66.507
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.07 Å3/Da / Density % sol: 40.63 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: Reservoir: 0.07 M sodium acetate, pH 4.6, 5.6% PEG 4000, 30% glycerol
Temp details: 14 and 20 C

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002
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: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 50154 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 27
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.3 / % possible all: 93

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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: 1.7→16.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.084 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 748 5 %RANDOM
Rwork0.16 ---
obs0.163 14199 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→16.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 49 161 1396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221304
X-RAY DIFFRACTIONr_bond_other_d0.0020.02903
X-RAY DIFFRACTIONr_angle_refined_deg1.5532.0111771
X-RAY DIFFRACTIONr_angle_other_deg0.94132206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70224.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35115235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0151511
X-RAY DIFFRACTIONr_chiral_restr0.090.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_nbd_refined0.2470.2284
X-RAY DIFFRACTIONr_nbd_other0.2020.21011
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2641
X-RAY DIFFRACTIONr_nbtor_other0.0840.2701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1061.51009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17321237
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5663644
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5474.5528
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 44
Rwork0.202 988
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)
12.04930.62160.15553.7196-1.21278.5640.0086-0.0917-0.1648-0.04660.21410.31120.4068-0.4648-0.22270.0241-0.03630.0007-0.14130.0430.09813.115-6.48611.318
22.0505-0.1833-0.85880.8701-0.0581.3665-0.0191-0.2265-0.030.00790.01250.0051-0.00910.08510.00660.0377-0.0129-0.0163-0.14830.01520.047616.4131.0826.941
30.27850.22790.47111.1261-0.57521.77890.020.1858-0.0946-0.0218-0.09650.03260.008-0.190.07650.0664-0.0095-0.0269-0.1314-0.01930.05719.563-0.065-5.275
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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