6N4Z

Tetragonal thermolysin (with 50% xylose) plunge cooled in liquid nitrogen to 77 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 ?
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A comparison of gas stream cooling and plunge cooling of macromolecular crystals.

Harrison, K.Wu, Z.Juers, D.H.

(2019) J Appl Crystallogr 52: 1222-1232

  • DOI: https://doi.org/10.1107/S1600576719010318
  • Primary Citation of Related Structures:  
    6N4W, 6N4Z

  • PubMed Abstract: 

    Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro-gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited.


  • Organizational Affiliation

    Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYP
Query on XYP

Download Ideal Coordinates CCD File 
L [auth A]
M [auth A]
N [auth A]
O [auth A]
P [auth A]
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [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]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 ?
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 41 21 2
Unit Cell:
Length ( ? )Angle ( ? )
a = 96.725¦Á = 90
b = 96.725¦Â = 90
c = 106.535¦Ã = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM0900248

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-13
    Changes: Data collection, Database references, Structure summary
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