8R44 | pdb_00008r44

PAS-GAF bidomain of Glycine max phytochrome A

PDB DOI: https://doi.org/10.2210/pdb8R44/pdb

Classification: PLANT PROTEIN
Organism(s): Glycine max
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-11-13 Released: 2025-01-08
Deposition Author(s): Guan, K., Nagano, S., Hughes, J.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.195 (Depositor), 0.203 (DCC)
R-Value Work:
0.175 (Depositor), 0.186 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Pr and Pfr structures of plant phytochrome A

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.

(2024) Research Square

DOI: https://doi.org/10.21203/rs.3.rs-4850459/v1

Macromolecule Content

Total Structure Weight: 82.31 kDa
Atom Count: 5,669
Modelled Residue Count: 628
Deposited Residue Count: 718
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytochrome A-2	A, B	359	Glycine max	Mutation(s): 0 Gene Names: PHYA2, GLYMA_20G090000
UniProt
Find proteins for B4YB07 (Glycine max) Explore B4YB07 Go to UniProtKB: B4YB07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4YB07
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC (Subject of Investigation/LOI) Query on CYC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	D [auth A], E [auth A], J [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]