2YZ8 | pdb_00002yz8

Crystal structure of the 32th Ig-like domain of human obscurin (KIAA1556)

• PDB DOI: https://doi.org/10.2210/pdb2YZ8/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-05-04 Released: 2008-05-06 
• Deposition Author(s): Saijo, S., Ohsawa, N., Nishino, A., Kishishita, S., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.261 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the 32th Ig-like domain of human obscurin (KIAA1556)

Saijo, S., Ohsawa, N., Nishino, A., Kishishita, S., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 10.84 kDa 
• Atom Count: 712 
• Modeled Residue Count: 90 
• Deposited Residue Count: 103 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Obscurin	A	103	Homo sapiens	Mutation(s): 0  Gene Names: OBSCN, KIAA1556 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VST9 (Homo sapiens) Explore Q5VST9  Go to UniProtKB:  Q5VST9
PHAROS:  Q5VST9 GTEx:  ENSG00000154358

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.261 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.358	α = 90
b = 43.358	β = 90
c = 102.316	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Saijo, S., Ohsawa, N., Nishino, A., Kishishita, S., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary