6FJ2 | pdb_00006fj2

Structure of Thermolysin solved from SAD data collected at the peak of the Zn absorption edge on ID30B

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.164 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.144 (Depositor) 
  • R-Value Observed: 
    0.145 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6FJ2

This is version 1.5 of the entry. See complete history. 

Literature

ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.

McCarthy, A.A., Barrett, R., Beteva, A., Caserotto, H., Dobias, F., Felisaz, F., Giraud, T., Guijarro, M., Janocha, R., Khadrouche, A., Lentini, M., Leonard, G.A., Lopez Marrero, M., Malbet-Monaco, S., McSweeney, S., Nurizzo, D., Papp, G., Rossi, C., Sinoir, J., Sorez, C., Surr, J., Svensson, O., Zander, U., Cipriani, F., Theveneau, P., Mueller-Dieckmann, C.

(2018) J Synchrotron Radiat 25: 1249-1260

  • DOI: https://doi.org/10.1107/S1600577518007166
  • Primary Citation Related Structures: 
    6FID, 6FJ2, 6FJ4, 6FJ6, 6FJ8, 6FJ9

  • PubMed Abstract: 

    ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).

    • Organizational Affiliation: 
    • European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France.

Macromolecule Content 

  • Total Structure Weight: 35.23 kDa 
  • Atom Count: 2,947 
  • 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 
Gene Names: npr
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
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS

Query on LYS


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

Query on VAL


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

Query on DMS


Download:Ideal Coordinates CCD File
G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
TMO

Query on TMO


Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
K [auth A]		trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N
ZN

Query on ZN


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

Query on CA


Download:Ideal Coordinates CCD File
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: 1.43 Å
  • R-Value Free:  0.164 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.144 (Depositor) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.717α = 90
b = 92.717β = 90
c = 128.621γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

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: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection
  • Version 1.2: 2018-07-18
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.4: 2019-02-20
    Changes: Data collection, Derived calculations
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations