3GE2 | pdb_00003ge2

Crystal structure of putative lipoprotein SP_0198 from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb3GE2/pdb

• Classification: LIPOPROTEIN
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-24 Released: 2009-03-17 
• Deposition Author(s): Kim, Y., Zhang, R., Joachimiak, G., Gornicki, P., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.224 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal Structure of Putative Lipoprotein SP_0198 from Streptococcus pneumoniae

Kim, Y., Zhang, R., Joachimiak, G., Gornicki, P., 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: 14.56 kDa 
• Atom Count: 817 
• Modeled Residue Count: 89 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein, putative	A	130	Streptococcus pneumoniae TIGR4	Mutation(s): 0
UniProt
Find proteins for A0A0H2UNA1 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UNA1  Go to UniProtKB:  A0A0H2UNA1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.20 Å
• R-Value Free:  0.224 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.007	α = 90
b = 106.007	β = 90
c = 64.613	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Kim, Y., Zhang, R., Joachimiak, G., Gornicki, P., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary