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)

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 2YZ8

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5VST9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

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

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Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.