3Q40 | pdb_00003q40

Sulphur SAD structure solution of proteinase K grown in SO4-less solution.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.183 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.138 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 
    0.140 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3Q40

This is version 1.3 of the entry. See complete history. 

Literature

Crystallization of Macromolecules in Selenate to Solve the Phase Problem

Jakoncic, J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 29.41 kDa 
  • Atom Count: 2,533 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 279 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NO3

Query on NO3


Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.183 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.138 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.863α = 90
b = 67.863β = 90
c = 101.853γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2011-06-22 
    • Deposition Author(s): Jakoncic, J.

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary