4G06

Crystal structure of protein SP_0782 (7-79) from Streptococcus pneumoniae complexed with ssDNA. Northeast Structural Genomics Consortium (NESG) target SPR104

• PDB DOI: https://doi.org/10.2210/pdb4G06/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-09 Released: 2012-07-25 
• Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Northeast Structural Genomics Consortium Target SpR104

Kuzin, A.P., Su, M., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

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: 19.43 kDa 
• Atom Count: 1,150 
• Modelled Residue Count: 136 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	79	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: SP_0782
UniProt
Find proteins for A0A0H2UPA7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UPA7  Go to UniProtKB:  A0A0H2UPA7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DT	C [auth A], D [auth A]	THYMIDINE-5'-MONOPHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-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: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.722	α = 90
b = 62.722	β = 90
c = 73.441	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary