5O8N | pdb_00005o8n

Structure of thermolysin at room temperature via a method of acoustically induced rotation.

• PDB DOI: https://doi.org/10.2210/pdb5O8N/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thermoproteolyticus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-06-13 Released: 2017-08-09 
• Deposition Author(s): Axford, D.N., Burton, C., Docker, P., Prince, M., Topham, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

An acoustic on-chip goniometer for room temperature macromolecular crystallography.

Burton, C.G., Axford, D., Edwards, A.M.J., Gildea, R.J., Morris, R.H., Newton, M.I., Orville, A.M., Prince, M., Topham, P.D., Docker, P.T.

(2017) Lab Chip 17: 4225-4230

• PubMed: 29124258 
• DOI: https://doi.org/10.1039/c7lc00812k
• Primary Citation Related Structures: 
  5O8N


• PubMed Abstract: 
  

  This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

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Organizational Affiliation: 
• Aston Institute of Material Research, Aston University, Birmingham B4 7ET, UK.

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: 34.81 kDa 
• Atom Count: 2,593 
• Modeled 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], M [auth A], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.552	α = 90
b = 93.552	β = 90
c = 129.753	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
cctbx.prime	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Axford, D.N., Burton, C., Docker, P., Prince, M., Topham, P.D.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references
• Version 1.2: 2017-12-13
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description