5WR5

Thermolysin, liganded form with cryo condition 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

Naitow, H.Matsuura, Y.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Yabashi, M.Tanaka, R.Tanaka, T.Sugahara, M.Kobayashi, J.Nango, E.Iwata, S.Kunishima, N.

(2017) Acta Crystallogr D Struct Biol 73: 702-709

  • DOI: 10.1107/S2059798317008919
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX ...

    Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.


    Organizational Affiliation

    Bio-Specimen Platform Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Geobacillus stearothermophilusMutation(s): 0 
Gene Names: nprS (nprM)
EC: 3.4.24.27
Find proteins for P43133 (Geobacillus stearothermophilus)
Go to UniProtKB:  P43133
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
NX6
Query on NX6

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Download CCD File 
A
N-[(benzyloxy)carbonyl]-L-aspartic acid
C12 H13 N O6
XYXYXSKSTZAEJW-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.246α = 90.00
b = 92.246β = 90.00
c = 129.718γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release