2IDL | pdb_00002idl

Crystal Structure of Conserved Protein of Unknown Function from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2IDL/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-09-15 Released: 2006-10-17 
• Deposition Author(s): Nocek, B., Wu, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of conserved hypothetical protein from Streptococcus pneumoniae TIGR4

Nocek, B., Wu, R., Abdullah, J., 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: 26.32 kDa 
• Atom Count: 2,041 
• Modeled Residue Count: 229 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	117	Streptococcus pneumoniae TIGR4	Mutation(s): 0
UniProt
Find proteins for A0A0H2UPY9 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UPY9  Go to UniProtKB:  A0A0H2UPY9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.665	α = 90
b = 62.359	β = 100.92
c = 63.415	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Nocek, B., Wu, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-10-17
  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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations