6FJ2

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

• PDB DOI: https://doi.org/10.2210/pdb6FJ2/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thermoproteolyticus
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2018-01-19 Released: 2018-01-31 
• Deposition Author(s): McCarthy, A.A., Mueller-Dieckmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.164 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

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

• PubMed: 29979188 
• DOI: https://doi.org/10.1107/S1600577518007166
• Primary Citation of Related Structures:  
  6FID, 6FJ2, 6FJ4, 6FJ6, 6FJ8, 6FJ9


• 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 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).

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.23 kDa 
• Atom Count: 2,947 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	316	Bacillus thermoproteolyticus	Mutation(s): 0  Gene Names: npr EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	M [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL	L [auth A]	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
DMS	G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
TMO	H [auth A], I [auth A], J [auth A], K [auth A]	trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.164 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/542

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.717	α = 90
b = 92.717	β = 90
c = 128.621	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): McCarthy, A.A., Mueller-Dieckmann, C.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection
• Version 1.2: 2018-07-18
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2018-08-08
  Changes: Data collection, Database references
• Version 1.4: 2019-02-20
  Changes: Data collection, Derived calculations
• Version 1.5: 2024-05-08
  Changes: Data collection, Database references, Derived calculations