3MTK | pdb_00003mtk

X-Ray Structure of Diguanylate cyclase/phosphodiesterase from Caldicellulosiruptor saccharolyticus, Northeast Structural Genomics Consortium Target ClR27C

• PDB DOI: https://doi.org/10.2210/pdb3MTK/pdb

• Classification: TRANSFERASE
• Organism(s): Caldicellulosiruptor saccharolyticus DSM 8903
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-30 Released: 2010-06-02 
• Deposition Author(s): Kuzin, A., Abashidze, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.270 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target ClR27C

Kuzin, A., Abashidze, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.43 kDa 
• Atom Count: 2,670 
• Modelled Residue Count: 325 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diguanylate cyclase/phosphodiesterase	A, B	178	Caldicellulosiruptor saccharolyticus DSM 8903	Mutation(s): 0  Gene Names: Csac_0821
UniProt
Find proteins for A4XHQ4 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XHQ4  Go to UniProtKB:  A4XHQ4

Small Molecules

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: 2.24 Å
• R-Value Free:  0.270 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.546	α = 90
b = 60.946	β = 94.95
c = 56.173	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Kuzin, A., Abashidze, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Structure summary