3KDQ

Crystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.

• PDB DOI: https://doi.org/10.2210/pdb3KDQ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-10-23 Released: 2009-11-10 
• Deposition Author(s): Zhang, R., Wu, R., Tan, K., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Literature

Crystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.

Zhang, R., Wu, R., Tan, K., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D8  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.15 kDa 
• Atom Count: 4,939 
• Modelled Residue Count: 609 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized conserved protein	A, B, C, D	154	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: Corynebacterium diphtheriae, DIP1984
UniProt
Find proteins for Q6NFB0 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NFB0  Go to UniProtKB:  Q6NFB0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.676	α = 90
b = 132.484	β = 90
c = 176.314	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Zhang, R., Wu, R., Tan, K., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance