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- PDB-2v1a: N- and C-terminal helices of oat LOV2 (404-546) are involved in l... -

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Basic information

Entry
Database: PDB / ID: 2v1a
TitleN- and C-terminal helices of oat LOV2 (404-546) are involved in light-induced signal transduction (room temperature (293K) 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


protein kinase activity / ATP binding / metal ion binding
Protein kinase, ATP binding site / Protein kinase domain profile. / PAC domain profile. / PAS domain / PAS-associated, C-terminal / Protein kinase domain / PAC motif / Serine/threonine-protein kinase, active site / Protein kinase-like domain superfamily / PAS repeat profile. ...Protein kinase, ATP binding site / Protein kinase domain profile. / PAC domain profile. / PAS domain / PAS-associated, C-terminal / Protein kinase domain / PAC motif / Serine/threonine-protein kinase, active site / Protein kinase-like domain superfamily / PAS repeat profile. / PAS domain superfamily / Protein kinase domain / PAS domain / Protein kinases ATP-binding region signature. / Serine/Threonine protein kinases active-site signature.
NPH1-1
Biological speciesAVENA SATIVA (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 22, 2007 / Release: Dec 11, 2007
RevisionDateData content typeGroupProviderType
1.0Dec 11, 2007Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelAdvisory / Version format compliance

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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)17,3074
Polymers16,6671
Non-polymers6413
Water2,576143
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)35.706, 57.155, 67.395
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/peptide 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 / Flavin mononucleotide
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O / Water
Sequence detailsPHE403 (VECTOR RESIDUES) 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: 2.15 Å3/Da / Density % sol: 42.8 % / 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: 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: 1.65→50 Å / Num. obs: 57554 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 30
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 5.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V0U
Resolution: 1.65→15.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.93 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 843 5.1 %RANDOM
Rwork0.156 ---
Obs0.158 15778 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 43 143 1359
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.010.0221272
r_bond_other_d0.0010.02876
r_angle_refined_deg1.2521731
r_angle_other_deg0.86732140
r_dihedral_angle_1_deg5.5645157
r_dihedral_angle_2_deg29.99924.54566
r_dihedral_angle_3_deg12.65715231
r_dihedral_angle_4_deg12.2491511
r_chiral_restr0.0790.2194
r_gen_planes_refined0.0050.021395
r_gen_planes_other0.0010.02250
r_nbd_refined0.210.2224
r_nbd_other0.1930.2940
r_nbtor_refined0.1790.2639
r_nbtor_other0.0820.2670
r_xyhbond_nbd_refined0.1420.276
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.2630.25
r_symmetry_vdw_other0.2990.245
r_symmetry_hbond_refined0.1290.220
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it1.1111.5993
r_mcbond_other
r_mcangle_it1.13121210
r_mcangle_other
r_scbond_it2.463634
r_scbond_other
r_scangle_it3.5414.5514
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.196 67
Rwork0.157 1166
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.94352.4138-2.90216.9683-1.76848.99590.02920.0387-0.0934-0.05070.11440.56980.2525-0.6813-0.1436-0.0861-0.0383-0.0341-0.02510.0307-0.0262.987-6.06410.231
21.4084-0.2829-0.48251.1555-0.18691.31640.0172-0.09070.00980.0442-0.0294-0.0223-0.0590.06510.0122-0.0237-0.0134-0.0165-0.04380.0008-0.064216.6211.1557.14
32.1354-0.4745-0.54841.13130.00194.03590.00130.0580.0402-0.03560.05890.0202-0.0175-0.0407-0.0602-0.0019-0.0076-0.043-0.055-0.0093-0.08199.59-0.236-5.114
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDAuth seq-ID
11403 - 414
22415 - 516
33517 - 546

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