3DNZ

Thermolysin by LB nanotemplate method before high X-Ray dose on ESRF ID14-2 beamline

• PDB DOI: https://doi.org/10.2210/pdb3DNZ/pdb

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


• Deposited: 2008-07-03 Released: 2009-07-07 
• Deposition Author(s): Pechkova, E., Tripathi, S.K., Nicolini, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 

Literature

Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective

Pechkova, E., Tripathi, S.K., Nicolini, C.

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: 34.85 kDa 
• Atom Count: 2,686 
• 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  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
LYS	H [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL	G [auth A]	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.535	α = 90
b = 92.535	β = 90
c = 128.628	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Pechkova, E., Tripathi, S.K., Nicolini, C.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-12-25
  Changes: Data collection, Derived calculations
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations