6FJ2

Structure of Thermolysin solved from SAD data collected at the peak of the Zn absorption edge on ID30B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.

McCarthy, A.A.Barrett, R.Beteva, A.Caserotto, H.Dobias, F.Felisaz, F.Giraud, T.Guijarro, M.Janocha, R.Khadrouche, A.Lentini, M.Leonard, G.A.Lopez Marrero, M.Malbet-Monaco, S.McSweeney, S.Nurizzo, D.Papp, G.Rossi, C.Sinoir, J.Sorez, C.Surr, J.Svensson, O.Zander, U.Cipriani, F.Theveneau, P.Mueller-Dieckmann, C.

(2018) J Synchrotron Radiat 25: 1249-1260

  • DOI: 10.1107/S1600577518007166
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be const ...

    ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France.




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

Download SDF File 
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
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

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Download CCD File 
A
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
TMO
Query on TMO

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Download CCD File 
A
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 92.717α = 90.00
b = 92.717β = 90.00
c = 128.621γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
CRANK2phasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection
  • Version 1.2: 2018-07-18
    Type: Data collection, Database references, Derived calculations
  • Version 1.3: 2018-08-08
    Type: Data collection, Database references
  • Version 1.4: 2019-02-20
    Type: Data collection, Derived calculations