3DNZ | pdb_00003dnz

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.267 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3DNZ

This is version 1.3 of the entry. See complete history. 

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.

Macromolecule Content 

  • Total Structure Weight: 34.85 kDa 
  • Atom Count: 2,686 
  • Modeled Residue Count: 316 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thermolysin316Bacillus thermoproteolyticusMutation(s): 0 
EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS

Query on LYS


Download:Ideal Coordinates CCD File
H [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL

Query on VAL


Download:Ideal Coordinates CCD File
G [auth A]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
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 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.535α = 90
b = 92.535β = 90
c = 128.628γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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