4Z1R | pdb_00004z1r

Crystal structure of collagen-like peptide at 1.27 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4Z1R/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-03-27 Released: 2015-11-18 
• Deposition Author(s): Plonska-Brzezinska, M.E., Czyrko, J., Brus, D.M., Imierska, M., Brzezinski, K.
• Funding Organization(s): National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Triple helical collagen-like peptide interactions with selected polyphenolic compounds.

Plonska-Brzezinska, M.E., Bobrowska, D.M., Sharma, A., Rodziewicz, P., Tomczyk, M., Czyrko, J., Brzezinski, K.

(2015) RSC Adv 5: 95443-95453

• DOI: https://doi.org/10.1039/c5ra15469c

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.11 kDa 
• Atom Count: 686 
• Modeled Residue Count: 78 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen-like peptide	A, B, C	30	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	A, B, C	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34z1r

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.573	α = 90
b = 13.939	β = 94.59
c = 24.981	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Plonska-Brzezinska, M.E., Czyrko, J., Brus, D.M., Imierska, M., Brzezinski, K.

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Funding Organization	Location	Grant Number
National Science Centre	Poland	2011/01/B/ST5/06051

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2020-04-22
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description