3IDU | pdb_00003idu

Crystal Structure of the CARDB domain of the PF1109 protein in complex with di-metal ions from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR193A

• PDB DOI: https://doi.org/10.2210/pdb3IDU/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-21 Released: 2009-08-04 
• Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.212 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Northeast Structural Genomics Consortium Target PfR193A

Forouhar, F., Neely, H., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

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: 29.14 kDa 
• Atom Count: 1,995 
• Modeled Residue Count: 226 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	127	Pyrococcus furiosus	Mutation(s): 0  Gene Names: PF1109
UniProt
Find proteins for Q8U1U6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1U6  Go to UniProtKB:  Q8U1U6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth B], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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: 1.70 Å
• R-Value Free:  0.212 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.551	α = 90
b = 72.665	β = 93.44
c = 58.456	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., 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: 2016-09-28
  Changes: Data collection
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection
• Version 1.6: 2024-11-20
  Changes: Structure summary