3FX3 | pdb_00003fx3

Structure of a putative cAMP-binding regulatory protein from Silicibacter pomeroyi DSS-3

• PDB DOI: https://doi.org/10.2210/pdb3FX3/pdb

• Classification: cAMP-binding protein
• Organism(s): Ruegeria pomeroyi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-19 Released: 2009-03-24 
• Deposition Author(s): Cuff, M.E., Zhou, M., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Structure of a putative cAMP-binding regulatory protein from Silicibacter pomeroyi DSS-3

Cuff, M.E., Zhou, M., Freeman, L., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.56 kDa 
• Atom Count: 3,892 
• Modeled Residue Count: 449 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic nucleotide-binding protein	A, B	237	Ruegeria pomeroyi	Mutation(s): 0  Gene Names: SPOA0323
UniProt
Find proteins for Q5LKQ8 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LKQ8  Go to UniProtKB:  Q5LKQ8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.20 Å
• R-Value Free:  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.728	α = 90
b = 137.728	β = 90
c = 94.626	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Cuff, M.E., Zhou, M., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary