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- PDB-8r45: Phytochromobilin-adducted PAS-GAF bidomain of Glycine max phytoch... -

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Basic information

Entry
Database: PDB / ID: 8r45
TitlePhytochromobilin-adducted PAS-GAF bidomain of Glycine max phytochrome A
ComponentsPhytochrome A-2
KeywordsPLANT PROTEIN / phytochrome / phycocyanobilin (PCB)
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
Chem-O6E / Phytochrome A-2
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGuan, K. / Chen, P. / Nagano, 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
DepositionNov 13, 2023Deposition 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,4205
Polymers80,0532
Non-polymers1,3683
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-25 kcal/mol
Surface area28000 Å2
Unit cell
Length a, b, c (Å)55.542, 112.526, 68.370
Angle α, β, γ (deg.)90.000, 92.078, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4YB07
#2: Chemical ChemComp-O6E / 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 0.04 M Ethylene glycols (0.01M Diethylene glycol; 0.01M Triethylene glycol; 0.01M Tetraethylene glycol; 0.01M Pentaethylene glycol); 0.1 M Tris (base); BICINE pH 9.0; 21% Precipitant Mix (7% ...Details: 0.04 M Ethylene glycols (0.01M Diethylene glycol; 0.01M Triethylene glycol; 0.01M Tetraethylene glycol; 0.01M Pentaethylene glycol); 0.1 M Tris (base); BICINE pH 9.0; 21% Precipitant Mix (7% v/v MPD; 7% PEG 1000; 7% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.86→42.34 Å / Num. obs: 70335 / % possible obs: 99.92 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 12.88
Reflection shellResolution: 1.86→1.926 Å / Num. unique obs: 7013 / CC1/2: 0.592

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→42.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.584 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.192 3578 5.087 %
Rwork0.1693 66756 -
all0.17 --
obs-70334 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.988 Å2
Baniso -1Baniso -2Baniso -3
1--0.503 Å20 Å2-0.03 Å2
2--0.381 Å2-0 Å2
3---0.124 Å2
Refinement stepCycle: LAST / Resolution: 1.86→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 99 465 5543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125214
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165004
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6637069
X-RAY DIFFRACTIONr_angle_other_deg1.5131.57811547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.745630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.705550
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.27152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20510883
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.985102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9610207
X-RAY DIFFRACTIONr_chiral_restr0.0770.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021111
X-RAY DIFFRACTIONr_nbd_refined0.2230.2999
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24446
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22484
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22781
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2363
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.212
X-RAY DIFFRACTIONr_nbd_other0.2280.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3180.218
X-RAY DIFFRACTIONr_mcbond_it3.1562.692532
X-RAY DIFFRACTIONr_mcbond_other3.1472.6912532
X-RAY DIFFRACTIONr_mcangle_it4.7214.7973155
X-RAY DIFFRACTIONr_mcangle_other4.7264.8013156
X-RAY DIFFRACTIONr_scbond_it4.1743.3872682
X-RAY DIFFRACTIONr_scbond_other4.1733.3872683
X-RAY DIFFRACTIONr_scangle_it6.4645.9483913
X-RAY DIFFRACTIONr_scangle_other6.4635.9483914
X-RAY DIFFRACTIONr_lrange_it8.91430.1945762
X-RAY DIFFRACTIONr_lrange_other8.89328.9025640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.9080.3092500.2744946X-RAY DIFFRACTION99.9808
1.908-1.960.2562640.2464761X-RAY DIFFRACTION100
1.96-2.0170.2522380.2254677X-RAY DIFFRACTION100
2.017-2.0790.2332380.214528X-RAY DIFFRACTION99.9581
2.079-2.1470.2252440.1954398X-RAY DIFFRACTION100
2.147-2.2220.2172120.1824268X-RAY DIFFRACTION100
2.222-2.3060.2112460.1654056X-RAY DIFFRACTION100
2.306-2.40.1812100.1533962X-RAY DIFFRACTION100
2.4-2.5060.2132030.1553760X-RAY DIFFRACTION100
2.506-2.6280.1862030.1523660X-RAY DIFFRACTION100
2.628-2.770.1991790.1553422X-RAY DIFFRACTION100
2.77-2.9370.1721630.1563280X-RAY DIFFRACTION99.9419
2.937-3.1390.1921620.1673054X-RAY DIFFRACTION99.9689
3.139-3.3890.1781260.1722889X-RAY DIFFRACTION99.9668
3.389-3.710.1821530.172622X-RAY DIFFRACTION100
3.71-4.1440.1831430.1482373X-RAY DIFFRACTION99.9603
4.144-4.7780.1341220.1222112X-RAY DIFFRACTION99.9553
4.778-5.8350.1741030.1581778X-RAY DIFFRACTION99.9469
5.835-8.180.145720.1681409X-RAY DIFFRACTION100
8.18-42.340.211470.197801X-RAY DIFFRACTION98.8345
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)
10.9062-0.0385-0.1010.03020.03110.25150.0561-0.0721-0.0771-0.0023-0.003-0.0189-0.04130.0262-0.05310.0114-0.01670.00270.04050.00310.031916.150514.21222.6455
20.104-0.1657-0.11310.7522-0.08970.3183-0.01120.0397-0.0033-0.0450.0085-0.05770.0298-0.07540.00270.0218-0.01750.01950.0275-0.01640.03560.83521.562-6.5903
Refinement TLS groupSelection: ALL

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