3IPN | pdb_00003ipn

Crystal Structure of fluorine and methyl modified collagen: (mepFlpgly)7

• PDB DOI: https://doi.org/10.2210/pdb3IPN/pdb

• Classification: STRUCTURAL PROTEIN
• Mutation(s): No 


• Deposited: 2009-08-18 Released: 2010-02-02 
• Deposition Author(s): Satyshur, K.A., Shoulders, M.D., Raines, R.T., Forest, K.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.258 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.173 (DCC) 

Starting Model: experimental

Literature

Stereoelectronic and steric effects in side chains preorganize a protein main chain.

Shoulders, M.D., Satyshur, K.A., Forest, K.T., Raines, R.T.

(2010) Proc Natl Acad Sci U S A 107: 559-564

• PubMed: 20080719 
• DOI: https://doi.org/10.1073/pnas.0909592107
• Primary Citation Related Structures: 
  3IPN


• PubMed Abstract: 
  

  Preorganization is shown to endow a protein with extraordinary conformational stability. This preorganization is achieved by installing side-chain substituents that impose stereoelectronic and steric effects that restrict main-chain torsion angles. Replacing proline residues in (ProProGly)(7) collagen strands with 4-fluoroproline and 4-methylproline leads to the most stable known triple helices, having T ( m ) values that are increased by > 50 degrees C. Differential scanning calorimetry data indicate an entropic basis to the hyperstability, as expected from an origin in preorganization. Structural data at a resolution of 1.21 A reveal a prototypical triple helix with insignificant deviations to its main chain, even though 2/3 of the residues are nonnatural. Thus, preorganization of a main chain by subtle changes to side chains can confer extraordinary conformational stability upon a protein without perturbing its structure.

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Organizational Affiliation: 
• Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.25 kDa 
• Atom Count: 994 
• Modeled Residue Count: 118 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-natural Collagen	A, B, C, D, E, F	21	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO3	G [auth A], H [auth B], I [auth D], J [auth F]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FP9	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H8 F N O2		PRO
MP8	A, B, C, D, E, F	L-PEPTIDE LINKING	C6 H11 N O2		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.258 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.173 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.4	α = 90
b = 25.3	β = 90.05
c = 61.9	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Satyshur, K.A., Shoulders, M.D., Raines, R.T., Forest, K.T.

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary