3HP7 | pdb_00003hp7

Putative hemolysin from Streptococcus thermophilus.

• PDB DOI: https://doi.org/10.2210/pdb3HP7/pdb

• Classification: structural genomics, unknown function
• Organism(s): Streptococcus thermophilus LMG 18311
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-06-03 Released: 2009-06-16 
• Deposition Author(s): Osipiuk, J., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

X-ray crystal structure of putative hemolysin from Streptococcus thermophilus.

Osipiuk, J., Hatzos, C., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.47 kDa 
• Atom Count: 2,687 
• Modeled Residue Count: 275 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin, putative	A	291	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: stu1215
UniProt
Find proteins for Q5M3Z4 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M3Z4  Go to UniProtKB:  Q5M3Z4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	B [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-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: 1.53 Å
• R-Value Free:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.958	α = 90
b = 81.713	β = 90
c = 95.537	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Osipiuk, J., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-06-16
  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: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary