5FSJ

Structure of thermolysin prepared by the 'soak-and-freeze' method under 45 bar of oxygen pressure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.105 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology.

Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

(2016) J Appl Crystallogr 49: 1478


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THERMOLYSIN316Bacillus thermoproteolyticusMutation(s): 0 
EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS
Download Ideal Coordinates CCD File 
C [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL
Query on VAL
Download Ideal Coordinates CCD File 
B [auth A]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
J [auth A],
K [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
OXY
Query on OXY
Download Ideal Coordinates CCD File 
I [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.105 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.922α = 90
b = 92.922β = 90
c = 130.252γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Structure summary
  • Version 1.2: 2018-02-21
    Changes: Advisory, Database references, Structure summary
  • Version 2.0: 2018-06-20
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description