5WR4 | pdb_00005wr4

Thermolysin, SFX unliganded form with oil-based carrier

• PDB DOI: https://doi.org/10.2210/pdb5WR4/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Geobacillus stearothermophilus
• Mutation(s): No 


• Deposited: 2016-11-29 Released: 2017-08-16 
• Deposition Author(s): Kunishima, N., Naitow, H., Matsuura, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

Naitow, H., Matsuura, Y., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Tanaka, R., Tanaka, T., Sugahara, M., Kobayashi, J., Nango, E., Iwata, S., Kunishima, N.

(2017) Acta Crystallogr D Struct Biol 73: 702-709

• PubMed: 28777085 
• DOI: https://doi.org/10.1107/S2059798317008919
• Primary Citation Related Structures: 
  5WR2, 5WR3, 5WR4, 5WR5, 5WR6


• PubMed Abstract: 
  

  Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.

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Organizational Affiliation: 
• Bio-Specimen Platform Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
XFEL Research and Development Division, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
SACLA Science Research Group, RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

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: 34.59 kDa 
• Atom Count: 2,765 
• 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	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: nprS, nprM EC: 3.4.24.27
UniProt
Find proteins for P43133 (Geobacillus stearothermophilus) Explore P43133  Go to UniProtKB:  P43133

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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: 2.10 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1375422

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.67	α = 90
b = 93.67	β = 90
c = 130.95	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Kunishima, N., Naitow, H., Matsuura, Y.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Refinement description