3PZ8 | pdb_00003pz8

Crystal structure of Dvl1-DIX(Y17D) mutant

PDB DOI: https://doi.org/10.2210/pdb3PZ8/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-12-14 Released: 2010-12-29
Deposition Author(s): Dan, Q.J., Chen, L., Zhang, Y.Y., Liu, Y.T., Wu, J.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.230 (Depositor), 0.229 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3PZ8

This is version 1.2 of the entry. See complete history.

Literature

Molecular basis of WNT activation via the DIX-domain protein CCD1

Liu, Y.T., Dan, Q.J., Wang, J.W., Feng, Y.G., Chen, L., Liang, J., Li, Q.X., Lin, S.C., Wang, Z.X., Wu, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 95.1 kDa
Atom Count: 5,409
Modeled Residue Count: 660
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-1	A, B, C, D, E A, B, C, D, E, F, G, H	106	Mus musculus	Mutation(s): 2 Gene Names: Dvl1, Dvl
UniProt
Find proteins for P51141 (Mus musculus) Explore P51141 Go to UniProtKB: P51141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51141
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.265 (Depositor), 0.264 (DCC)
R-Value Work: 0.230 (Depositor), 0.229 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.687	α = 90
b = 106.78	β = 90
c = 265.957	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-12-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, 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.