3ICL | pdb_00003icl

X-Ray Structure of Protein (EAL/GGDEF domain protein) from M.capsulatus, Northeast Structural Genomics Consortium Target McR174C

• PDB DOI: https://doi.org/10.2210/pdb3ICL/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methylococcus capsulatus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-07-17 Released: 2009-08-04 
• Deposition Author(s): Kuzin, A., Chen, Y., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Foote, E.L., Wang, H., 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: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target McR174C

Kuzin, A., Chen, Y., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Foote, E.L., Wang, H., 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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.65 kDa 
• Atom Count: 2,577 
• Modeled Residue Count: 317 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EAL/GGDEF domain protein	A, B	171	Methylococcus capsulatus	Mutation(s): 1  Gene Names: MCA0337
UniProt
Find proteins for Q60BX6 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore Q60BX6  Go to UniProtKB:  Q60BX6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.672	α = 90
b = 75.95	β = 90
c = 95.196	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
Auto-Rickshaw	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Kuzin, A., Chen, Y., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Foote, E.L., Wang, H., 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: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2021-10-13
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Structure summary