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- PDB-8r44: PAS-GAF bidomain of Glycine max phytochrome A -

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Basic information

Entry
Database: PDB / ID: 8r44
TitlePAS-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 / 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. / 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phytochrome A-2
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsGuan, K. / Nagano, S. / Hughes, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1078 Germany
CitationJournal: 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

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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)82,30710
Polymers80,0532
Non-polymers2,2558
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.287, 111.812, 68.273
Angle α, β, γ (deg.)90.000, 92.308, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 595 molecules

#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: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Ethylene glycols (0.3M diethylene glycol; 0.3M triethylene glycol; 0.3M tetraethylene glycol; 0.3M pentaethylene glycol), 0.1 M Tris (base);BICINE pH 8.5, 30% v/v Precipitant Mix 1 ...Details: 0.12 M Ethylene glycols (0.3M diethylene glycol; 0.3M triethylene glycol; 0.3M tetraethylene glycol; 0.3M pentaethylene glycol), 0.1 M Tris (base);BICINE pH 8.5, 30% v/v Precipitant Mix 1 (20% v/v PEG 500 MME; 10 % w/v PEG 20000)

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Data collection

DiffractionMean temperature: 40 K / Ambient temp details: liquid helium cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.896 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.896 Å / Relative weight: 1
ReflectionResolution: 1.58→43.841 Å / Num. obs: 112709 / % possible obs: 99.58 % / Redundancy: 3.7 % / CC1/2: 0.998 / Net I/σ(I): 12.84
Reflection shellResolution: 1.58→1.636 Å / Num. unique obs: 11216 / CC1/2: 0.418

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→43.841 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.167 / SU B: 4.154 / SU ML: 0.068 / Average fsc free: 0.9659 / Average fsc work: 0.97 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1945 5372 4.767 %
Rwork0.175 107308 -
all0.176 --
obs-112680 99.614 %
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: 28.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.064 Å20 Å20.128 Å2
2--0.004 Å20 Å2
3---0.049 Å2
Refinement stepCycle: LAST / Resolution: 1.58→43.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 158 587 5669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125202
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164966
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6817032
X-RAY DIFFRACTIONr_angle_other_deg0.5261.57311474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.465524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06210874
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.48210204
X-RAY DIFFRACTIONr_chiral_restr0.0820.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021080
X-RAY DIFFRACTIONr_nbd_refined0.2320.21039
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24398
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22483
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22738
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2471
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.213
X-RAY DIFFRACTIONr_nbd_other0.2260.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.214
X-RAY DIFFRACTIONr_mcbond_it2.8842.3962506
X-RAY DIFFRACTIONr_mcbond_other2.8822.3962506
X-RAY DIFFRACTIONr_mcangle_it4.6134.2663122
X-RAY DIFFRACTIONr_mcangle_other4.6134.2693123
X-RAY DIFFRACTIONr_scbond_it4.0373.0492696
X-RAY DIFFRACTIONr_scbond_other4.0383.0492697
X-RAY DIFFRACTIONr_scangle_it6.2585.3353910
X-RAY DIFFRACTIONr_scangle_other6.2575.3363911
X-RAY DIFFRACTIONr_lrange_it9.36127.1265898
X-RAY DIFFRACTIONr_lrange_other9.30926.3755697
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
1.58-1.6210.2943840.30779460.30683550.9350.92899.70080.308
1.621-1.6650.2863780.28977160.28981140.9420.9499.75350.289
1.665-1.7140.2813410.27275030.27378580.9470.9599.82180.268
1.714-1.7660.263950.23672930.23776940.9580.96499.9220.227
1.766-1.8240.2353570.2170460.21274120.9670.97199.87860.196
1.824-1.8880.2173870.19368440.19572320.9710.97699.98620.176
1.888-1.9590.2573230.24365520.24369510.9540.95998.90660.221
1.959-2.0390.2023500.17663400.17766960.9750.98199.91040.157
2.039-2.1290.1873360.16660910.16764310.9760.98499.93780.15
2.129-2.2330.1942630.17158410.17261120.9760.98299.86910.154
2.233-2.3530.2222480.1854560.18258610.960.97697.32130.157
2.353-2.4960.192770.14652350.14855160.9780.98799.92750.134
2.496-2.6670.1812560.14449340.14552010.980.98799.78850.133
2.667-2.880.1872500.14845900.1548480.9790.98799.8350.141
2.88-3.1540.1812010.16142400.16144430.9790.98599.9550.157
3.154-3.5240.1941800.16738580.16840500.9790.98499.70370.166
3.524-4.0650.1541610.15433660.15435740.9850.98698.6850.159
4.065-4.9670.141350.13329030.13330460.990.9999.73740.148
4.967-6.980.1881020.18822570.18823640.9830.98599.78850.203
6.98-43.8410.172480.17912970.17913540.9820.9899.33530.208
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)
10.79490.0017-0.01920.0392-0.02240.22280.0355-0.0581-0.09580.00120.0104-0.0077-0.05590.0337-0.04590.0168-0.01870.00870.0535-0.00220.026315.385814.583622.5775
20.0797-0.085-0.08220.7239-0.0710.1913-0.01080.0448-0.0217-0.04250.0149-0.04090.0053-0.0581-0.00410.0185-0.01550.02030.0331-0.02110.0390.49832.0293-6.1759
Refinement TLS groupSelection: ALL

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