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- PDB-6tby: Phycocyanobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB -

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Basic information

Entry
Database: PDB / ID: 6tby
TitlePhycocyanobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB
ComponentsPhytochrome
KeywordsPLANT PROTEIN / phytochrome
Function / homology
Function and homology information


protein-phytochromobilin linkage / red, far-red light phototransduction / detection of visible light / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / protein homodimerization activity
Similarity search - Function
Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain ...Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PHYCOCYANOBILIN / DI(HYDROXYETHYL)ETHER / Phytochrome B / Phytochrome B
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNagano, S. / Guan, K. / Shenkutie, S.M. / Hughes, J.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 1078 Germany
CitationJournal: Nat.Plants / Year: 2020
Title: Structural insights into photoactivation and signalling in plant phytochromes.
Authors: Nagano, S. / Guan, K. / Shenkutie, S.M. / Feiler, C. / Weiss, M. / Kraskov, A. / Buhrke, D. / Hildebrandt, P. / Hughes, J.
History
DepositionNov 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Phytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9397
Polymers38,8901
Non-polymers1,0496
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The PAS-GAF bidomain behaves as monomer in solution. The apparent molecular weight calculated from the elution peak from the gel filtraction chromatography corresponds to that of the monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-18 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.738, 134.738, 46.543
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11AAA-742-

HOH

21AAA-743-

HOH

31AAA-745-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Phytochrome / / Phycocyanobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB


Mass: 38889.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: PHYB, SORBI_3001G394400 / Plasmid: pPROLar.A122 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6S527, UniProt: P93527*PLUS

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Non-polymers , 5 types, 151 molecules

#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: (100 mM Tris/HCl pH 8.5, 500 mM NaCl, 9% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→44.1 Å / Num. obs: 44840 / % possible obs: 99.4 % / Redundancy: 20.3 % / Biso Wilson estimate: 39.819 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.026 / Rrim(I) all: 0.086 / Χ2: 0.98 / Net I/σ(I): 22.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 21.3 % / Rmerge(I) obs: 2.726 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2647 / CC1/2: 0.646 / Rpim(I) all: 0.858 / Rrim(I) all: 2.858 / Χ2: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSMar 15 2019data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUR
Resolution: 1.8→44.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.633 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2118 2198 4.903 %
Rwork0.1789 --
all0.181 --
obs-44827 99.326 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20.001 Å20 Å2
2--0.002 Å2-0 Å2
3----0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 71 145 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132611
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172471
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.6363535
X-RAY DIFFRACTIONr_angle_other_deg1.441.5675692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.46119.787141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69515412
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg10.06153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.951524
X-RAY DIFFRACTIONr_chiral_restr0.10.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined0.210.2536
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22321
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21259
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4350.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.30.222
X-RAY DIFFRACTIONr_nbd_other0.220.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2410.220
X-RAY DIFFRACTIONr_mcbond_it3.7993.9191279
X-RAY DIFFRACTIONr_mcbond_other3.7933.9141278
X-RAY DIFFRACTIONr_mcangle_it5.1385.8421594
X-RAY DIFFRACTIONr_mcangle_other5.1375.8471595
X-RAY DIFFRACTIONr_scbond_it5.0064.4811330
X-RAY DIFFRACTIONr_scbond_other5.0044.4811331
X-RAY DIFFRACTIONr_scangle_it7.4816.4941938
X-RAY DIFFRACTIONr_scangle_other7.4796.4941939
X-RAY DIFFRACTIONr_lrange_it9.70648.0692848
X-RAY DIFFRACTIONr_lrange_other9.70948.0022837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3141390.3131670.31133080.7790.76699.93950.287
1.847-1.8970.3621620.31830190.3232110.7340.74999.06570.294
1.897-1.9520.3411700.29729660.29931600.8030.83599.24050.261
1.952-2.0120.2641580.22728810.22830390.890.911000.19
2.012-2.0780.221470.20327650.20329300.930.92999.38570.173
2.078-2.1510.2031110.19527450.19528690.9350.94199.54690.164
2.151-2.2320.2471490.21626110.21827700.920.9299.6390.182
2.232-2.3220.2981440.22325250.22726700.8940.92499.96250.189
2.322-2.4250.2191140.17424180.17625370.9340.9599.80290.153
2.425-2.5430.2141280.17723180.17924480.9410.95199.91830.155
2.543-2.6810.2381020.17322280.17523330.9320.95199.87140.157
2.681-2.8420.199970.17719580.17821910.9510.95493.79280.163
2.842-3.0380.2111140.16819250.1720830.9480.95797.88770.161
3.038-3.280.1911260.16618130.16819390.9550.9611000.165
3.28-3.5910.186760.16417200.16517960.960.9671000.168
3.591-4.0120.158580.14715500.14716080.9740.9731000.156
4.012-4.6260.153630.12413940.12614570.9750.9781000.139
4.626-5.650.219570.15511720.15812290.9650.971000.171
5.65-7.9250.226550.199210.1929770.9510.95599.89760.21
7.925-44.1030.191280.2275320.2255700.9670.94798.24560.266

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