5A3Y

SAD structure of Thermolysin obtained by multi crystal data collection

• PDB DOI: https://doi.org/10.2210/pdb5A3Y/pdb

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


• Deposited: 2015-06-04 Released: 2015-11-11 
• Deposition Author(s): Zander, U., Bourenkov, G., Popov, A.N., de Sanctis, D., McCarthy, A.A., Svensson, O., Round, E.S., Gordeliy, V.I., Mueller-Dieckmann, C., Leonard, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.166 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

Literature

Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines.

Zander, U., Bourenkov, G., Popov, A.N., De Sanctis, D., Svensson, O., Mccarthy, A.A., Round, E., Gordeliy, V., Mueller-Dieckmann, C., Leonard, G.A.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2328

• PubMed: 26527148 
• DOI: https://doi.org/10.1107/S1399004715017927
• Primary Citation of Related Structures:  
  5A3Y, 5A3Z, 5A44, 5A45, 5A47


• PubMed Abstract: 
  

  Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.

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Organizational Affiliation: 

Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.88 kDa 
• Atom Count: 2,810 
• Modelled Residue Count: 316 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THERMOLYSIN	A	548	Bacillus thermoproteolyticus	Mutation(s): 0  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	C [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL	B [auth A]	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
DMS	I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
TMO	J [auth A], K [auth A]	trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.166 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.874	α = 90
b = 92.874	β = 90
c = 129.167	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Zander, U., Bourenkov, G., Popov, A.N., de Sanctis, D., McCarthy, A.A., Svensson, O., Round, E.S., Gordeliy, V.I., Mueller-Dieckmann, C., Leonard, G.A.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Advisory, Data collection, Derived calculations, Other
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other