2ID8

Crystal structure of Proteinase K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

What can be done with a good crystal and an accurate beamline?

Wang, J.Dauter, M.Dauter, Z.

(2006) Acta Crystallogr.,Sect.D 62: 1475-1483

  • DOI: 10.1107/S0907444906038534

  • PubMed Abstract: 
  • X-ray single-wavelength anomalous diffraction (SAD) data from a crystal of proteinase K were collected using synchrotron radiation of 0.98 A wavelength at SER-CAT 22-ID beamline, Advanced Photon Source, Argonne National Laboratory. At this wavelength ...

    X-ray single-wavelength anomalous diffraction (SAD) data from a crystal of proteinase K were collected using synchrotron radiation of 0.98 A wavelength at SER-CAT 22-ID beamline, Advanced Photon Source, Argonne National Laboratory. At this wavelength, the expected Bijvoet ratio resulting from the presence of one calcium, one chloride and ten S atoms in the 279-residue protein is extremely small at approximately 0.46%. The direct-methods program SHELXD located 11 anomalous sites using data truncated to 2 A resolution. SHELXE was used to produce an easily interpretable electron-density map. This study shows that an accurate beamline and a good-quality crystal provide the possibility of successfully using a very weak anomalous signal of sulfur measured at a short wavelength for phasing a protein structure, even if a small degree of radiation damage is present.


    Organizational Affiliation

    SAIC-Frederick Inc., Basic Research Program, Argonne National Laboratory, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteinase K
A
279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Parengyodontium album)
Go to UniProtKB:  P06873
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
2DB
Query on 2DB

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Download CCD File 
A
(S)-(2,3-DIHYDROXYPROPOXY)TRIHYDROXYBORATE
C3 H10 B O6
KLKDDPLTQSQDLA-VKHMYHEASA-N
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.550α = 90.00
b = 67.550β = 90.00
c = 106.880γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXDphasing
SHELXL-97refinement
SHELXmodel building
HKL-2000data reduction
SHELXEmodel building
SERGUIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance