6R26 | pdb_00006r26

The photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 
    0.276 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structures of the photosensory core module of bacteriophytochrome Agp1 reveal pronounced structural flexibility of this protein in the red-absorbing Pr state

Scheerer, P., Schmidt, A., Nagano, S., Qureshi, B., Szczepek, M., Sauthof, L., Michael, N., Inomata, K., Lamparter, T., Krauss, N.

To be published.

Macromolecule Content 

  • Total Structure Weight: 57.1 kDa 
  • Atom Count: 3,530 
  • Modeled Residue Count: 479 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacteriophytochrome protein510Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: Atu1990
EC: 2.7.13.3
UniProt
Find proteins for Q7CY45 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q7CY45 
Go to UniProtKB:  Q7CY45
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CY45
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JQ2
(Subject of Investigation/LOI)

Query on JQ2


Download:Ideal Coordinates CCD File
B [auth A]3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3,7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid
C34 H38 N4 O6
ZPENGPJFMYEJSJ-DPTABBBISA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free:  0.276 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.445α = 90
b = 174.445β = 90
c = 79.067γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB498-B2
German Research FoundationGermanySFB1078-B6
German Research FoundationGermanyLA 799/18-1
German Research FoundationGermanyKR 2034/1-1
German Research FoundationGermanyDFG under Germanys Excellence Strategy - UniSysCat - 390540038
German Research FoundationGermanyDFG Cluster of Excellence - UniCat

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary