4DUI | pdb_00004dui

DARPIN D1 binding to tubulin beta chain (not in complex)

• PDB DOI: https://doi.org/10.2210/pdb4DUI/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-22 Released: 2013-02-27 
• Deposition Author(s): Pecqueur, L., Duellberg, C., Dreier, B., Wang, Q., Jiang, C., Pluckthun, A., Surrey, T., Gigant, B., Knossow, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.149 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.125 (Depositor) 

Starting Model: experimental

Literature

An Anti-Tubulin Darpin Caps the Microtubule Plus-End

Pecqueur, L., Duellberg, C., Dreier, B., Wang, Q., Jiang, C., Pluckthun, A., Surrey, T., Gigant, B., Knossow, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.56 kDa 
• Atom Count: 1,501 
• Modeled Residue Count: 165 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1	A	169	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A], D [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	B [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SME	A	L-PEPTIDE LINKING	C5 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.149 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.4	α = 90
b = 43.4	β = 90
c = 143.12	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Pecqueur, L., Duellberg, C., Dreier, B., Wang, Q., Jiang, C., Pluckthun, A., Surrey, T., Gigant, B., Knossow, M.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description