4HJF

EAL domain of phosphodiesterase PdeA in complex with c-di-GMP and Ca++

• PDB DOI: https://doi.org/10.2210/pdb4HJF/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-12 Released: 2012-10-31 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Massa, C., Schirmer, T., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.214 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Crystal structure of EAL domain from Caulobacter crescentus in complex with c-di-GMP and Ca

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Massa, C., Schirmer, T., Joachimiak, A., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 37.55 kDa 
• Atom Count: 2,292 
• Modelled Residue Count: 263 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF family protein	A	340	Caulobacter vibrioides CB15	Mutation(s): 0  Gene Names: 943316, CC_3396
UniProt
Find proteins for Q9A310 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9A310  Go to UniProtKB:  Q9A310

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	D [auth A]	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
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.214 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M34HJF

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.202	α = 90
b = 63.186	β = 90
c = 66.19	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Massa, C., Schirmer, T., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2016-08-31
  Changes: Structure summary
• Version 1.2: 2016-10-12
  Changes: Structure summary
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2023-12-06
  Changes: Data collection