5DTH | pdb_00005dth

Crystal structure of MUPP1 PDZ8 domain from rattus norvegicus

PDB DOI: https://doi.org/10.2210/pdb5DTH/pdb

Classification: SIGNALING PROTEIN, CELL ADHESION
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-18 Released: 2016-09-14
Deposition Author(s): Li, J., Lv, Y., Zhu, H., Liu, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.265 (Depositor), 0.282 (DCC)
R-Value Work:
0.225 (Depositor), 0.239 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure and biochemical characteristics of MUPP1 PDZ8 domain from rattus norregicus

Lv, Y., Li, J., Zhu, H., Liu, W.

To be published.

Macromolecule Content

Total Structure Weight: 48.93 kDa
Atom Count: 3,420
Modeled Residue Count: 428
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multiple PDZ domain protein	A, B, C, D	111	Rattus norvegicus	Mutation(s): 0 Gene Names: Mpdz, Mupp1
UniProt
Find proteins for O55164 (Rattus norvegicus) Explore O55164 Go to UniProtKB: O55164
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55164
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.265 (Depositor), 0.282 (DCC)
R-Value Work: 0.225 (Depositor), 0.239 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.104	α = 90
b = 39.242	β = 92.73
c = 134.449	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.