3A1M | pdb_00003a1m

A fusion protein of a beta helix region of gene product 5 and the foldon region of bacteriophage T4

• PDB DOI: https://doi.org/10.2210/pdb3A1M/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-11 Released: 2010-04-21 
• Deposition Author(s): Yokoi, N., Suzuki, A., Hikage, T., Koshiyama, T., Terauchi, M., Yutani, K., Kanamaru, S., Arisaka, F., Yamane, T., Watanabe, Y., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Construction of Robust Bio-nanotubes using the Controlled Self-Assembly of Component Proteins of Bacteriophage T4

Yokoi, N., Inaba, H., Terauchi, M., Stieg, A.Z., Sanghamitra, N.J., Koshiyama, T., Yutani, K., Kanamaru, S., Arisaka, F., Hikage, T., Suzuki, A., Yamane, T., Gimzewski, J.K., Watanabe, Y., Kitagawa, S., Ueno, T.

(2010) Small 6: 1873-1879

• PubMed: 20661999 
• DOI: https://doi.org/10.1002/smll.201000772
• Primary Citation of Related Structures:  
  3A1M

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Nagoya university, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 89.18 kDa 
• Atom Count: 4,820 
• Modeled Residue Count: 590 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chimera of thrombin cleavage site, Tail-associated lysozyme, Fibritin	A, B, C, D, E, F	139	Tequatrovirus T4	Mutation(s): 1  EC: 3.2.1.17
UniProt
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104  Go to UniProtKB:  P10104
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009  Go to UniProtKB:  P16009
UniProt Groups	P16009P10104

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	G [auth A], H [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.268 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.814	α = 90
b = 57.01	β = 103.9
c = 136.594	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Yokoi, N., Suzuki, A., Hikage, T., Koshiyama, T., Terauchi, M., Yutani, K., Kanamaru, S., Arisaka, F., Yamane, T., Watanabe, Y., Ueno, T.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-06-28
  Changes: Source and taxonomy
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description