2FIM | pdb_00002fim

Structure of the C-terminal domain of Human Tubby-like protein 1

• PDB DOI: https://doi.org/10.2210/pdb2FIM/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-29 Released: 2006-02-07 
• Deposition Author(s): Hallberg, B.M., Ogg, D., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hogbom, M., Holmberg-Schiavone, L., Kotenyova, T., Kursula, P., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Persson, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Structure of the C-terminal domain of Human Tubby-like protein 1

Persson, C., Ogg, D., Thorsell, A.G., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hogbom, M., Holmberg-Schiavone, L., Kotenyova, T., Kursula, P., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Sagemark, J., Stenmark, P., Sundstrom, M., Van Den Berg, S., Weigelt, J., Hallberg, B.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.36 kDa 
• Atom Count: 3,841 
• Modeled Residue Count: 456 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubby related protein 1	A, B	276	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O00294 (Homo sapiens) Explore O00294  Go to UniProtKB:  O00294
PHAROS:  O00294 GTEx:  ENSG00000112041

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3DP	C [auth A]	3-(N,N-DIMETHYLOCTYLAMMONIO)PROPANESULFONATE C13 H29 N O3 S QZRAABPTWGFNIU-UHFFFAOYSA-N
SO4	D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.96	α = 90
b = 85.15	β = 92.93
c = 58.79	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-07 
Deposition Author(s): Hallberg, B.M., Ogg, D., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hogbom, M., Holmberg-Schiavone, L., Kotenyova, T., Kursula, P., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Persson, C.

Revision History  

• Version 1.0: 2006-02-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations