9P17 | pdb_00009p17

Thermolysin Room-Temperature In-Situ, Shipped


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.183 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.160 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9P17

This is version 1.0 of the entry. See complete history

Literature

Does crossing the pond affect crystal quality?

Campomizzi, C.S.Snell, M.E.Mikolajek, H.Sandy, J.Sanchez-Weatherby, J.Budziszewski, G.R.Russi, S.Howells Jr., R.Cohen, A.Hough, M.A.Bowman, S.E.J.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.06.12.659325
  • Primary Citation Related Structures: 
    9P12, 9P13, 9P14, 9P15, 9P16, 9P17

  • PubMed Abstract: 

    Room-temperature (RT) X-ray diffraction experiments enable us to investigate protein dynamics, efficiently probe fragment binding, and perform time-resolved crystallography experiments. The Versatile Macromolecular Crystallography in-situ (VMXi) beamline at Diamond Light Source (DLS) in the United Kingdom specializes in the collection of RT X-ray diffraction data in situ directly from crystallization trays without any manipulation of protein crystals, improving crystal integrity for fragile crystals. While many X-ray sources are now equipped to grow crystals on site for in-situ experiments, to date there has been no comprehensive analysis that we are aware of on the effect of shipping crystals on plates at ambient temperature for RT data collection, while the equivalent methodology for cryo-cooled crystals is well established. Here we examine the impact of shipping on crystals grown on MiTeGen In Situ-1 plates at the University of Buffalo Hauptman Woodward Research Institute (UB-HWI) in Buffalo, NY, United States transatlantic to DLS in Didcot, United Kingdom. We utilized the Stanford Synchrotron Radiation Lightsource (SSRL) Blue Box Thermal Shipper (Blue Box), which can maintain temperature for up to 168 hours, to ship crystallization plates at room temperature from UB-HWI to DLS. We hypothesized that long-distance shipping might compromise data quality through mechanical stress or temperature fluctuations. Instead, we found that room-temperature data collected at VMXi showed no significant differences for crystals set up at UB-HWI and shipped relative to crystals set up on site in the UK. High-resolution structures were successfully determined for all proteins in the study, demonstrating that long-distance shipment of crystals at non-cryogenic temperatures is feasible without compromising diffraction quality. This study provides a proof-of-concept workflow for expanding access to room-temperature crystallography worldwide, enabling more researchers to leverage cutting-edge techniques without needing to grow crystals on site.


  • Organizational Affiliation
    • University at Buffalo Hauptman Woodward Institute, 700 Ellicott Street, Buffalo, NY, 14203, United States.

Macromolecule Content 

  • Total Structure Weight: 34.72 kDa 
  • Atom Count: 2,673 
  • 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
Thermolysin316Geobacillus stearothermophilusMutation(s): 0 
Gene Names: nprSnprM
EC: 3.4.24.27
UniProt
Find proteins for P43133 (Geobacillus stearothermophilus)
Explore P43133 
Go to UniProtKB:  P43133
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43133
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
H [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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],
G [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.032α = 90
b = 93.032β = 90
c = 130.452γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
Cootmodel building
xia2.multiplexdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM141273

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release