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- PDB-6tl4: Photosensory module (PAS-GAF-PHY) of Glycine max phyB -

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Basic information

Entry
Database: PDB / ID: 6tl4
TitlePhotosensory module (PAS-GAF-PHY) of Glycine max phyB
ComponentsPhytochrome
KeywordsPLANT PROTEIN / phytochrome
Function / homology
Function and homology information


protein-phycocyanobilin linkage / red, far-red light phototransduction / detection of visible light / : / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / protein homodimerization activity / nucleus
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 / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Phytochrome B-2
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionDec 1, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4852
Polymers59,8961
Non-polymers5891
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The PAS-GAF-PHY fragment behaves as monomer in solution. The apparent molecular weight calculated from the elution peak from the gel filtraction chromatography corresponds ...Evidence: gel filtration, The PAS-GAF-PHY fragment 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 area1350 Å2
ΔGint-19 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.269, 102.269, 222.918
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Phytochrome /


Mass: 59896.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 100794865, GLYMA_15G140000 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I1MGE5
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 5.63 Å3/Da / Density % sol: 78.15 % / Description: Hexagonal bipyramid
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200mM MES, 200mM KSCN, 200mM LiCl2, 1% w/v gamma-PGA, 3% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.9→47.17 Å / Num. obs: 30704 / % possible obs: 99.9 % / Redundancy: 19.8 % / Biso Wilson estimate: 85.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.238 / Rpim(I) all: 0.077 / Rrim(I) all: 0.251 / Χ2: 1.01 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 19.9 % / Rmerge(I) obs: 5.838 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4420 / CC1/2: 0.591 / Rpim(I) all: 1.893 / Rrim(I) all: 6.14 / Χ2: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUR

4our


Resolution: 2.9→47.17 Å / SU ML: 0.4858 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4519
RfactorNum. reflection% reflection
Rfree0.2824 1550 5.09 %
Rwork0.257 --
obs0.2582 30475 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 121.82 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 43 2 3834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943919
X-RAY DIFFRACTIONf_angle_d1.39175330
X-RAY DIFFRACTIONf_chiral_restr0.0668604
X-RAY DIFFRACTIONf_plane_restr0.0083683
X-RAY DIFFRACTIONf_dihedral_angle_d18.3242575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.47021320.45692520X-RAY DIFFRACTION95.98
2.99-3.10.40091440.3792582X-RAY DIFFRACTION99.24
3.1-3.220.3711340.36232575X-RAY DIFFRACTION99.34
3.23-3.370.33611510.33862571X-RAY DIFFRACTION98.95
3.37-3.550.3541490.32792622X-RAY DIFFRACTION99.57
3.55-3.770.28981680.282573X-RAY DIFFRACTION99.56
3.77-4.060.29851490.25512616X-RAY DIFFRACTION99.78
4.06-4.470.28561540.2292620X-RAY DIFFRACTION99.78
4.47-5.120.18681170.21752704X-RAY DIFFRACTION99.89
5.12-6.440.32621250.25942704X-RAY DIFFRACTION99.68
6.45-47.170.21771270.21062838X-RAY DIFFRACTION99.33
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)
12.488654921460.471048081185-0.7998034888434.006759992592.192455069495.575556078620.172549483881-0.01334105936370.483054318-0.2130086884170.169222950124-0.217648723329-1.382471021060.445297426334-0.3330495750471.108149091960.3268665530410.03040345017180.764356899398-0.03141294892730.755693112182-27.4619134126-17.625205465925.009368246
21.88940907457-2.35400130975-0.7393485441374.598966621451.615295257820.497133182067-0.225832782289-0.402567225050.1955654032230.426803327310.649093125777-0.155233013534-0.05529902774340.339131446657-0.3299816682441.237630817010.445817747421-0.01617960411170.894121978354-0.05918359359310.660436033531-26.0336941315-34.857371119524.4978680915
31.03470192943-1.045165850320.4483340370854.46256580712-1.471191817794.484803958660.2880296856740.351797966329-0.090045277067-0.582008712352-0.430178158443-0.7505885449491.368447606870.9824600773210.1940977081541.106574231020.5137290629430.05549603502921.189397437760.01976795778220.680281326996-12.432769924-61.719091915113.1902966732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 345 )
2X-RAY DIFFRACTION2chain 'A' and (resid 346 through 448 or resid 700 through 702 )
3X-RAY DIFFRACTION3chain 'A' and (resid 449 through 618 )

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