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- PDB-9qzt: Room temperature structure of Glycine max phyA in Pfr/Pr ensemble -

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Basic information

Entry
Database: PDB / ID: 9qzt
TitleRoom temperature structure of Glycine max phyA in Pfr/Pr ensemble
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 / 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. / 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. / Histidine kinase/HSP90-like ATPase / 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. / Schultz, J.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 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
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein migrates as a dimer in gel filtration columns.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 0.991 / 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
PHENIX1.21rc1_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
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. atoms4803 0 86 138 5027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019852
X-RAY DIFFRACTIONf_angle_d1.331713365
X-RAY DIFFRACTIONf_chiral_restr0.07041521
X-RAY DIFFRACTIONf_plane_restr0.01311702
X-RAY DIFFRACTIONf_dihedral_angle_d16.16543709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.33191490.32592663X-RAY DIFFRACTION99.82
2.25-2.30.36791410.30122650X-RAY DIFFRACTION99.93
2.3-2.360.31821280.28612696X-RAY DIFFRACTION99.93
2.36-2.420.32611180.28072654X-RAY DIFFRACTION99.96
2.42-2.490.3821230.27992716X-RAY DIFFRACTION99.86
2.49-2.570.29181230.2572680X-RAY DIFFRACTION99.86
2.57-2.660.26391580.2372635X-RAY DIFFRACTION99.96
2.66-2.770.30671500.23392668X-RAY DIFFRACTION99.86
2.77-2.90.24811290.23112678X-RAY DIFFRACTION99.72
2.9-3.050.27331650.22142638X-RAY DIFFRACTION99.64
3.05-3.240.27031700.20512622X-RAY DIFFRACTION99.54
3.24-3.490.22111200.18942722X-RAY DIFFRACTION99.96
3.49-3.840.21851450.16052676X-RAY DIFFRACTION99.86
3.84-4.390.15961690.14052654X-RAY DIFFRACTION100
4.39-5.510.19561490.1442677X-RAY DIFFRACTION99.89
5.51-20.480.21391710.17382707X-RAY DIFFRACTION99.93

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