3CP3 | pdb_00003cp3

Crystal structure of conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb3CP3/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Corynebacterium diphtheriae NCTC 13129
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-03-31 Released: 2008-04-15 
• Deposition Author(s): Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae.

Kim, Y., Wu, R., Clancy, S., 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: 16.91 kDa 
• Atom Count: 1,191 
• Modeled Residue Count: 127 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	148	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0  Gene Names: DIP1874
UniProt
Find proteins for Q6NFL3 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NFL3  Go to UniProtKB:  Q6NFL3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	B [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.374	α = 90
b = 59.374	β = 90
c = 98.948	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description