7GR2 | pdb_00007gr2

Crystal Structure of PAS-GAF domain of the phytochrome from Deinococcus radiodurans at femto and picosecond timescales (144 fs)

PDB DOI: https://doi.org/10.2210/pdb7GR2/pdb
Deposition Group: G_1002281 (changed state) | Explore G_1002281

Classification: TRANSFERASE
Organism(s): Deinococcus radiodurans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-11-07 Released: 2025-10-01
Deposition Author(s): Shankar, M.K., Westenhoff, S.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.192 (Depositor), 0.192 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Crystal Structure of PAS-GAF domain of the phytochrome from Deinococcus radiodurans at femto and picosecond timescales

Shankar, M.K., Westenhoff, S.

To be published.

Macromolecule Content

Total Structure Weight: 75.63 kDa
Atom Count: 5,231
Modeled Residue Count: 628
Deposited Residue Count: 686
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome	A, B	343	Deinococcus radiodurans	Mutation(s): 0 Gene Names: bphP, DR_A0050 EC: 2.7.13.3
UniProt
Find proteins for Q9RZA4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RZA4 Go to UniProtKB: Q9RZA4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RZA4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBV (Subject of Investigation/LOI) Query on LBV Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid C₃₃ H₃₇ N₄ O₆ DKMLMZVDTGOEGU-ISEYCTJISA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.192 (Depositor), 0.192 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.95	α = 90
b = 116.5	β = 90
c = 117.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data scaling
CrystFEL	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	279944

Revision History (Full details and data files)

Version 1.0: 2025-10-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.