6TTR | pdb_00006ttr

Crystal Structure of the coiled coil and GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP

• PDB DOI: https://doi.org/10.2210/pdb6TTR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caulobacter vibrioides NA1000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-12-30 Released: 2021-01-13 
• Deposition Author(s): Holzschuh, F., Schirmer, T., Teixeira, R.D.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: other

Literature

Crystal structure of the coiled coil and GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP

Holzschuh, F., Schirmer, T., Teixeira, R.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.26 kDa 
• Atom Count: 3,092 
• Modeled Residue Count: 386 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF diguanylate cyclase DgcB	A, B	222	Caulobacter vibrioides NA1000	Mutation(s): 2  Gene Names: dgcB, CCNA_01926 EC: 2.7.7.65
UniProt
Find proteins for A0A0H3CAN8 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3CAN8  Go to UniProtKB:  A0A0H3CAN8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	D [auth A], E [auth A], F [auth B]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N
PO4	C [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.084	α = 90
b = 148.745	β = 90
c = 60.401	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Holzschuh, F., Schirmer, T., Teixeira, R.D.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A-166652

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description