2I5U | pdb_00002i5u

Crystal structure of DnaD domain protein from Enterococcus faecalis. Structural genomics target APC85179

• PDB DOI: https://doi.org/10.2210/pdb2I5U/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-08-25 Released: 2006-11-07 
• Deposition Author(s): Wu, R., Zhang, R., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.227 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

1.5 A crystal structure of a DnaD domain protein from Enterococcus Faecalis

Wu, R., Zhang, R., Bargassa, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.71 kDa 
• Atom Count: 749 
• Modeled Residue Count: 77 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaD domain protein	A	83	Enterococcus faecalis V583	Mutation(s): 2  Gene Names: DnaD
UniProt
Find proteins for Q830E8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830E8  Go to UniProtKB:  Q830E8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.227 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.795	α = 90
b = 48.795	β = 90
c = 32.795	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-07 
Deposition Author(s): Wu, R., Zhang, R., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-11-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary