5FSS

Structure of thermolysin prepared by the 'soak-and-freeze' method under 40 bar of krypton pressure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.5 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
A
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

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A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
KR
Query on KR

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A
KRYPTON
Kr
DNNSSWSSYDEUBZ-UHFFFAOYSA-N
 Ligand Interaction
VAL
Query on VAL

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A
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.749α = 90.00
b = 92.749β = 90.00
c = 128.995γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Structure summary
  • Version 1.2: 2017-05-10
    Type: Structure summary
  • Version 1.3: 2018-02-21
    Type: Database references, Structure summary
  • Version 1.4: 2018-02-28
    Type: Structure summary
  • Version 1.5: 2018-06-20
    Type: Advisory, Data collection, Derived calculations