3D0J | pdb_00003d0j

Crystal structure of conserved protein of unknown function CA_C3497 from Clostridium acetobutylicum ATCC 824

• PDB DOI: https://doi.org/10.2210/pdb3D0J/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Clostridium acetobutylicum ATCC 824
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-01 Released: 2008-07-01 
• Deposition Author(s): Kim, Y., Bigelow, L., Clancy, S., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal Structure of Conserved Protein of Unknown Function CA_C3497 from Clostridium acetobutylicum ATCC 824.

Kim, Y., Bigelow, L., Clancy, S., Abdullah, J., Joachimiak, A.

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: 16.92 kDa 
• Atom Count: 1,523 
• Modeled Residue Count: 138 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein CA_C3497	A	140	Clostridium acetobutylicum ATCC 824	Mutation(s): 0  Gene Names: CA_C3497
UniProt
Find proteins for Q97DI0 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97DI0  Go to UniProtKB:  Q97DI0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	B [auth A], C [auth A], D [auth A], E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.878	α = 90
b = 52.878	β = 90
c = 112.28	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXD	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Kim, Y., Bigelow, L., Clancy, S., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary