8C3I | pdb_00008c3i

Dark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome

PDB DOI: https://doi.org/10.2210/pdb8C3I/pdb

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

Deposited: 2022-12-24 Released: 2024-01-10
Deposition Author(s): Madan Kumar, S., Sebastian, W.
Funding Organization(s): European Research Council (ERC), Japan Agency for Medical Research and Development (AMED), Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.161 (Depositor), 0.162 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Dark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome

Madan Kumar, S., Sebastian, W.

To be published.

Macromolecule Content

Total Structure Weight: 75.63 kDa
Atom Count: 5,183
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 [auth B], B [auth A]	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 C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	C [auth B], D [auth A]	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 B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.161 (Depositor), 0.162 (DCC)
R-Value Observed: 0.163 (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 reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Madan Kumar, S.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	279944
Japan Agency for Medical Research and Development (AMED)	Japan	--
Academy of Finland	Finland	285461

Revision History (Full details and data files)

Version 1.0: 2024-01-10
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

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