5DLH | pdb_00005dlh

SFX structure of thermolysin

• PDB DOI: https://doi.org/10.2210/pdb5DLH/pdb

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


• Deposited: 2015-09-04 Released: 2015-11-18 
• Deposition Author(s): DeMirci, H.D., Sauter, N.K., Brewster, A.S., Kern, J.
• Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Serial Femtosecond Crystallography of Ribosome-Antibiotic and Photosystem II Complexes at Ambient Temperature using a Concentric Electrospinning Injector.

DeMirci, H.D.

To be published.

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: 2,531 
• 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: 2.25 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.794	α = 90
b = 93.794	β = 90
c = 132.243	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): DeMirci, H.D., Sauter, N.K., Brewster, A.S., Kern, J.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102520
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM095887

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2018-02-14
  Changes: Data collection
• Version 1.3: 2018-09-19
  Changes: Data collection
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2024-03-06
  Changes: Data collection, Database references, Derived calculations