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- PDB-9f4i: Room temperature structure of Glycine max phyA in Pfr -

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Basic information

Entry
Database: PDB / ID: 9f4i
TitleRoom temperature structure of Glycine max phyA in Pfr
ComponentsPhytochrome A-2
KeywordsPLANT PROTEIN / phytochrome / phyA / Glycine max
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 / Phytochrome, central region / PAS fold-2 / PAS fold / 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 / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS-associated, C-terminal / PAC 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 superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Phytochrome A-2
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNagano, S. / Hughes, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1078 Germany
Citation
Journal: Nat Commun / Year: 2025
Title: Pr and Pfr structures of plant phytochrome A.
Authors: Nagano, S. / von Stetten, D. / Guan, K. / Chen, P.Y. / Song, C. / Barends, T. / Weiss, M.S. / Feiler, C.G. / Dorner, K. / de Diego Martinez, I. / Schubert, R. / Bielecki, J. / Brings, L. / ...Authors: Nagano, S. / von Stetten, D. / Guan, K. / Chen, P.Y. / Song, C. / Barends, T. / Weiss, M.S. / Feiler, C.G. / Dorner, K. / de Diego Martinez, I. / Schubert, R. / Bielecki, J. / Brings, L. / Han, H. / Kharitonov, K. / Kim, C. / Kloos, M. / Koliyadu, J.C.P. / Koua, F.H.M. / Round, E. / Sarma, A. / Sato, T. / Schmidt, C. / Valerio, J. / Wrona, A. / Schulz, J. / de Wijn, R. / Letrun, R. / Bean, R. / Mancuso, A. / Heyne, K. / Hughes, J.
#1: Journal: Research Square / Year: 2024
Title: Pr and Pfr structures of plant phytochrome A
Authors: Hughes, J. / Nagano, S. / Guan, K. / Chen, P.Y. / von Stetten, D. / Song, C. / Barends, T. / Weiss, M. / Feiler, C. / Dorner, K. / de Diego, I. / Schubert, R. / Bielecki, J. / Brings, L. / ...Authors: Hughes, J. / Nagano, S. / Guan, K. / Chen, P.Y. / von Stetten, D. / Song, C. / Barends, T. / Weiss, M. / Feiler, C. / Dorner, K. / de Diego, I. / Schubert, R. / Bielecki, J. / Brings, L. / Kim, C. / Han, H. / Kharitonov, K. / Koliyadu, J. / Koua, F. / Round, E. / Sarma, A. / Sato, T. / Kloos, M. / Valerio, J. / Wrona, A. / Schmidt, C. / de Wijn, R. / Letrun, R. / Mancuso, A. / Bean, R. / Heyne, K. / Schulz, J.
History
DepositionApr 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 2, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytochrome A-2
B: Phytochrome A-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2304
Polymers80,0532
Non-polymers1,1772
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Please also refer to 8R44, 8R45, and 9ER4.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-65 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.450, 115.050, 69.800
Angle α, β, γ (deg.)90.000, 92.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Phytochrome A-2 / GmphyA2


Mass: 40026.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: PHYA2, GLYMA_20G090000 / Plasmid: pPCDF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4YB07
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 296 K / Method: batch mode / pH: 8.5
Details: 0.1 M Tris (base), BICINE pH 8.5, 18% v/v PEG 500MME 9% w/v PEG 20000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Aug 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 2.2→20.79 Å / Num. obs: 45135 / % possible obs: 100 % / Redundancy: 1282.2 % / Biso Wilson estimate: 47.56 Å2 / CC1/2: 0.9919 / CC star: 0.998 / R split: 0.1088 / Net I/σ(I): 7.88
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 965.1 % / Mean I/σ(I) obs: 0.71 / Num. unique obs: 45048 / CC1/2: 0.5686 / CC star: 0.8515 / R split: 1.084 / % possible all: 100
Serial crystallography sample deliveryDescription: GVDN / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: Crystal slurry, filtered / Flow rate: 20 µL/min
Power by: Shimadzu HPLC pumps LC-20AD) using 100 micrometer inner diameter tubing

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Processing

Software
NameVersionClassification
PHENIX1.21rc_5156refinement
CrystFELv.0.10.2data reduction
CrystFELPartialator v.0.10.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20.48 Å / SU ML: 0.3209 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: This refinement statistics derive from when the structure was refined as a triggered / dark state mixture, against the Light data. Therefore it may not agree well with R-values reported for ...Details: This refinement statistics derive from when the structure was refined as a triggered / dark state mixture, against the Light data. Therefore it may not agree well with R-values reported for the validation process (i.e. pure triggered state, against the Light data).
RfactorNum. reflection% reflection
Rfree0.2314 2308 5.12 %
Rwork0.1907 42736 -
obs0.1929 45044 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4734 0 0 132 4866
LS refinement shellResolution: 2.2→2.25 Å
RfactorNum. reflection% reflection
Rfree0.3237 --
Rwork0.3038 2812 -
obs--99.82 %

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