4HE5 | pdb_00004he5

Crystal structure of the selenomethionine variant of the C-terminal domain of Geobacillus thermoleovorans putative U32 peptidase

• PDB DOI: https://doi.org/10.2210/pdb4HE5/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Geobacillus thermoleovorans CCB_US3_UF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-03 Released: 2012-11-14 
• Deposition Author(s): Trillo-Muyo, S., Jasilionis, A., Domagalski, M.J., Chruszcz, M., Minor, W., Kuisiene, N., Arolas, J.L., Sola, M., Gomis-Ruth, F.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.170 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Literature

Ultratight crystal packing of a 10 kDa protein.

Trillo-Muyo, S., Jasilionis, A., Domagalski, M.J., Chruszcz, M., Minor, W., Kuisiene, N., Arolas, J.L., Sola, M., Gomis-Ruth, F.X.

(2013) Acta Crystallogr D Biol Crystallogr 69: 464-470

• PubMed: 23519421 
• DOI: https://doi.org/10.1107/S0907444912050135
• Primary Citation Related Structures: 
  4HE5, 4HE6


• PubMed Abstract: 
  

  While small organic molecules generally crystallize forming tightly packed lattices with little solvent content, proteins form air-sensitive high-solvent-content crystals. Here, the crystallization and full structure analysis of a novel recombinant 10 kDa protein corresponding to the C-terminal domain of a putative U32 peptidase are reported. The orthorhombic crystal contained only 24.5% solvent and is therefore among the most tightly packed protein lattices ever reported.

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Organizational Affiliation: 
• Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Spanish Research Council CSIC, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Spain.

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: 10.6 kDa 
• Atom Count: 777 
• Modeled Residue Count: 82 
• Deposited Residue Count: 89 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase family U32	A	89	Geobacillus thermoleovorans CCB_US3_UF5	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.15 Å
• R-Value Free:  0.170 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.55	α = 90
b = 45.55	β = 90
c = 60.9	γ = 120

Software Package:

Software Name	Purpose
ProDC	data collection
SHELX	model building
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Trillo-Muyo, S., Jasilionis, A., Domagalski, M.J., Chruszcz, M., Minor, W., Kuisiene, N., Arolas, J.L., Sola, M., Gomis-Ruth, F.X.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Database references
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary