4ZMM

GGDEF domain of Dcsbis complexed with c-di-GMP

• PDB DOI: https://doi.org/10.2210/pdb4ZMM/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-04 Released: 2016-05-04 
• Deposition Author(s): Chen, Y., Liu, C., Liu, S., Chi, K., Gu, L.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Crystal structure of Dcsbis GGDEF domain complexed with c-di-GMP

Chen, Y., Liu, C., Liu, S., Chi, K., Gu, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 50.97 kDa 
• Atom Count: 2,674 
• Modelled Residue Count: 325 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
diguanylate cyclase	A, B	223	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA2771 EC: 2.7.7.65
UniProt
Find proteins for Q9I072 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I072  Go to UniProtKB:  Q9I072

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	C [auth A], D [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.275	α = 90
b = 42.707	β = 106.75
c = 106.372	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Chen, Y., Liu, C., Liu, S., Chi, K., Gu, L.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2015CB150600

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-04-03
  Changes: Refinement description