4HE5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.,Sect.D 69: 464-470

  • DOI: 10.1107/S0907444912050135
  • Primary Citation of Related Structures:  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 1 ...

    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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidase family U32
A
89Geobacillus thermoleovorans CCB_US3_UF5N/A
Find proteins for G8N3E1 (Geobacillus thermoleovorans CCB_US3_UF5)
Go to UniProtKB:  G8N3E1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.141 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 45.550α = 90.00
b = 45.550β = 90.00
c = 60.900γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XDSdata reduction
ProDCdata collection
SHELXphasing
SHELXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references
  • Version 1.2: 2013-06-19
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description