2J9N

Robotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Operator Assisted Harvesting of Protein Crystals Using a Universal Micromanipulation Robot.

Viola, R.Carman, P.Walsh, J.Miller, E.Benning, M.Frankel, D.McPherson, A.Cudney, R.Rupp, B.

(2007) J.Appl.Crystallogr. 40: 539

  • DOI: 10.1107/S0021889807012149

  • PubMed Abstract: 
  • High-throughput crystallography has reached a level of automation where complete computer-assisted robotic crystallization pipelines are capable of cocktail preparation, crystallization plate setup, and inspection and interpretation of results. While ...

    High-throughput crystallography has reached a level of automation where complete computer-assisted robotic crystallization pipelines are capable of cocktail preparation, crystallization plate setup, and inspection and interpretation of results. While mounting of crystal pins, data collection and structure solution are highly automated, crystal harvesting and cryocooling remain formidable challenges towards full automation. To address the final frontier in achieving fully automated high-throughput crystallography, the prototype of an anthropomorphic six-axis universal micromanipulation robot (UMR) has been designed and tested; this UMR is capable of operator-assisted harvesting and cryoquenching of protein crystals as small as 10 microm from a variety of 96-well plates. The UMR is equipped with a versatile tool exchanger providing full operational flexibility. Trypsin crystals harvested and cryoquenched using the UMR have yielded a 1.5 A structure demonstrating the feasibility of robotic protein crystal harvesting.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATIONIC TRYPSIN
A
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UNKNOWN PEPTIDE
B
15N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UNKNOWN PEPTIDE
C
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
IPH
Query on IPH

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Download CCD File 
A
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B, C
L-PEPTIDE LINKINGC4 H9 N O2

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BDNKi: 31 - 39000 nM (100) BINDINGDB
BENKd: 20000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.924α = 90.00
b = 56.695β = 90.00
c = 66.054γ = 90.00
Software Package:
Software NamePurpose
SHAKEANDWARPphasing
EPMRphasing
BRUKERdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2012-06-20
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2016-12-28
    Type: Source and taxonomy
  • Version 1.3: 2017-07-05
    Type: Data collection