[English] 日本語
Yorodumi
- PDB-8r45: Phytochromobilin-adducted PAS-GAF bidomain of Glycine max phytoch... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more