1KTH | pdb_00001kth

The Anisotropic Refinement Of Kunitz Type Domain C5 at 0.95 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb1KTH/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2002-01-16 Released: 2002-02-06 
• Deposition Author(s): Arnoux, B., Ducruix, A., Prange, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 A).

Arnoux, B., Ducruix, A., Prange, T.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1252-1254

• PubMed: 12077460 
• DOI: https://doi.org/10.1107/s0907444902007333
• Primary Citation of Related Structures:  
  1KTH


• PubMed Abstract: 
  

  The C-terminal Kunitz-type domain from the alpha3 chain of human type VI collagen (C5), a single amino-acid residue chain with three disulfide bridges, was refined at 0.9 A resolution in a monoclinic form, space group P2(1) with one molecule per asymmetric unit, using data collected at cryogenic temperature (110 K). The average protein factor decreases from 21 A(2) at room temperature (RT) to 12 A(2) at cryotemperature (100 K, CT). The spatially close N- and C-termini remain highly disordered. The different structural motifs of C5 were analyzed in terms of rigid-body displacement (TLS analyses) and show dominant libration motion for the secondary structure.

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Organizational Affiliation: 

Laboratoire de Cristallographie et RMN Biologiques (UMR 8015 CNRS), Faculté de Pharmacie 4, Avenue de l'Observatoire, 75006 Paris, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.83 kDa 
• Atom Count: 566 
• Modelled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha 3(VI) chain	A	58	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P12111 (Homo sapiens) Explore P12111  Go to UniProtKB:  P12111
PHAROS:  P12111 GTEx:  ENSG00000163359

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.27	α = 90
b = 37.8	β = 109.42
c = 28.51	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-06 
Deposition Author(s): Arnoux, B., Ducruix, A., Prange, T.

Revision History  

• Version 1.0: 2002-02-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary