3V7B | pdb_00003v7b

Dip2269 protein from corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb3V7B/pdb
• Entry: 3V7B supersedes: 2I8G

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-20 Released: 2012-01-11 
• Deposition Author(s): Osipiuk, J., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.228 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Dip2269 protein from corynebacterium diphtheriae.

Osipiuk, J., Duggan, E., Clancy, S., Joachimiak, A.

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: 33.65 kDa 
• Atom Count: 2,528 
• Modeled Residue Count: 289 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	151	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP2269
UniProt
Find proteins for Q6NEK4 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEK4  Go to UniProtKB:  Q6NEK4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.74 Å
• R-Value Free:  0.228 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.002	α = 90
b = 66.752	β = 90
c = 70.287	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Osipiuk, J., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 2I8G

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary