3ZI6

Structure of thermolysin solved by SAD from data collected by Direct Data Collection (DDC) using the GRob robot goniometer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Recent Progress in Robot-Based Systems for Crystallography and Their Contribution to Drug Discovery.

Ferrer, J.L.Larive, N.A.Bowler, M.W.Nurizzo, D.

(2013) Expert Opin.Drug Discov. 8: 835


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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Download SDF File 
Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
VAL
Query on VAL

Download SDF File 
Download CCD File 
A
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.754α = 90.00
b = 92.754β = 90.00
c = 129.224γ = 120.00
Software Package:
Software NamePurpose
SHELXCDEphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-01-04 
  • Released Date: 2013-05-01 
  • Deposition Author(s): Bowler, M.W.

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references, Refinement description, Structure summary
  • Version 1.2: 2013-07-03
    Type: Database references
  • Version 1.3: 2018-06-20
    Type: Advisory, Data collection, Derived calculations