3S83 | pdb_00003s83

EAL domain of phosphodiesterase PdeA

• PDB DOI: https://doi.org/10.2210/pdb3S83/pdb

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


• Deposited: 2011-05-27 Released: 2011-06-29 
• 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: 1.34 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of EAL domain from Caulobacter crescentus CB15

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Massa, C., Schirmer, T., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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: 28.52 kDa 
• Atom Count: 2,419 
• Modeled Residue Count: 256 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF family protein	A	259	Caulobacter vibrioides	Mutation(s): 0  Gene Names: 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-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: 1.34 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.193	α = 90
b = 46.963	β = 96.32
c = 63.77	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
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: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-27
  Changes: Structure summary
• Version 1.3: 2016-08-31
  Changes: Structure summary
• Version 1.4: 2016-10-12
  Changes: Structure summary
• Version 1.5: 2017-11-08
  Changes: Refinement description
• Version 1.6: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary