3U2E | pdb_00003u2e

EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++

• PDB DOI: https://doi.org/10.2210/pdb3U2E/pdb
• NAKB: 3U2E

• Classification: lyase/RNA
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-03 Released: 2011-10-12 
• 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: 2.32 Å
• R-Value Free: 
  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

EAL domain from Caulobacter crescentus in complex with 5'-pGpG and Mg++

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

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

Macromolecule Content 

• Total Structure Weight: 58.93 kDa 
• Atom Count: 4,190 
• Modeled Residue Count: 519 
• Deposited Residue Count: 526 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF family protein	A, B	261	Caulobacter vibrioides CB15	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*G)-3')	C, D	2	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33U2E

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.144	α = 90
b = 75.154	β = 90
c = 129.066	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
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: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2016-08-31
  Changes: Structure summary
• Version 1.2: 2016-10-12
  Changes: Structure summary
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-12-06
  Changes: Data collection
• Version 1.6: 2024-11-06
  Changes: Structure summary