3BH1 | pdb_00003bh1

Crystal structure of protein DIP2346 from Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb3BH1/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Corynebacterium diphtheriae NCTC 13129
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-27 Released: 2007-12-11 
• Deposition Author(s): Patskovsky, Y., Sridhar, V., Bonanno, J.B., Gilmore, M., Iizuka, M., Groshong, C., Gheyi, T., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.271 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Crystal structure of protein DIP2346 from Corynebacterium diphtheriae.

Patskovsky, Y., Sridhar, V., Bonanno, J.B., Gilmore, M., Iizuka, M., Groshong, C., Gheyi, T., Wasserman, S.R., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 226.02 kDa 
• Atom Count: 15,333 
• Modeled Residue Count: 1,942 
• Deposited Residue Count: 2,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0371 protein DIP2346	A, B, C, D	507	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0  Gene Names: DIP2346
UniProt
Find proteins for Q6NEC9 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEC9  Go to UniProtKB:  Q6NEC9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.271 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.453	α = 90
b = 138.936	β = 116.49
c = 98.266	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Patskovsky, Y., Sridhar, V., Bonanno, J.B., Gilmore, M., Iizuka, M., Groshong, C., Gheyi, T., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references