3IJD | pdb_00003ijd

Uncharacterized protein Cthe_2304 from Clostridium thermocellum binds two copies of 5-methyl-5,6,7,8-tetrahydrofolic acid

• PDB DOI: https://doi.org/10.2210/pdb3IJD/pdb

• Classification: structural genomics, unknown function
• Organism(s): Acetivibrio thermocellus ATCC 27405
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-04 Released: 2009-09-01 
• Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Ozyurt, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Uncharacterized protein Cthe_2304 from Clostridium thermocellum binds two copies of 5-methyl-5,6,7,8-tetrahydrofolic acid

Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Ozyurt, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.46 kDa 
• Atom Count: 4,725 
• Modeled Residue Count: 571 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	315	Acetivibrio thermocellus ATCC 27405	Mutation(s): 0  Gene Names: Cthe_2304
UniProt
Find proteins for A3DHS7 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DHS7  Go to UniProtKB:  A3DHS7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2F	C [auth A], D [auth A], E [auth B], F [auth B]	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID C20 H25 N7 O6 ZNOVTXRBGFNYRX-STQMWFEESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.581	α = 94.68
b = 52.368	β = 97.68
c = 60.918	γ = 90.57

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Ozyurt, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references