4GDO | pdb_00004gdo

Structure of a fragment of the rod domain of plectin

PDB DOI:&nbsphttps://doi.org/10.2210/pdb4GDO/pdb

Classification:&nbspSTRUCTURAL PROTEIN
Organism(s):&nbspHomo sapiens
Expression System:&nbspEscherichia coli BL21(DE3)
Mutation(s):&nbspNo&nbsp

Deposited:&nbsp2012-08-01&nbspReleased:&nbsp2013-09-11&nbsp
Deposition Author(s):&nbspDe Pereda, J.M., Buey, R.M., Uson, I., Sammito, M.D., De Marino, I.

Experimental Data Snapshot

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.70 Å
R-Value Free:&nbsp
0.248 (Depositor), 0.256 (DCC)&nbsp
R-Value Work:&nbsp
0.213 (Depositor), 0.218 (DCC)&nbsp
R-Value Observed:&nbsp
0.215&nbsp(Depositor)&nbsp

wwPDB Validation&nbsp3D Report&nbspFull Report

Validation slider image for 4GDO

This is version 1.3 of the entry. See complete&nbsphistory.&nbsp

Literature

Exploiting tertiary structure through local folds for crystallographic phasing.

Sammito, M.,&nbspMillan, C.,&nbspRodriguez, D.D.,&nbspde Ilarduya, I.M.,&nbspMeindl, K.,&nbspDe Marino, I.,&nbspPetrillo, G.,&nbspBuey, R.M.,&nbspde Pereda, J.M.,&nbspZeth, K.,&nbspSheldrick, G.M.,&nbspUson, I.

(2013) Nat Methods&nbsp10: 1099-1101

PubMed:&nbsp24037245&nbspSearch on PubMed
DOI:&nbsphttps://doi.org/10.1038/nmeth.2644
Primary Citation Related Structures:&nbsp
4GDO, 4GN0

PubMed Abstract:&nbsp
We describe an algorithm for phasing protein crystal X-ray diffraction data that identifies, retrieves, refines and exploits general tertiary structural information from small fragments available in the Protein Data Bank. The algorithm successfully phased, through unspecific molecular replacement combined with density modification, all-helical, mixed alpha-beta, and all-beta protein structures. The method is available as a software implementation: Borges.

Organizational Affiliation

Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain.

Macromolecule Content&nbsp

Total Structure Weight: 29.28 kDa&nbsp
Atom Count: 1,816&nbsp
Modeled Residue Count: 223&nbsp
Deposited Residue Count: 258&nbsp
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plectin	A, B, C, D, E A, B, C, D, E, F	43	Homo sapiens	Mutation(s): 0&nbsp Gene Names:&nbspPLEC,&nbspPLEC1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspQ15149&nbsp(Homo sapiens) Explore&nbspQ15149&nbsp Go to UniProtKB: &nbspQ15149
PHAROS: &nbspQ15149 GTEx: &nbspENSG00000178209&nbsp
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15149
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.70 Å
R-Value Free:&nbsp 0.248 (Depositor), 0.256 (DCC)&nbsp
R-Value Work:&nbsp 0.213 (Depositor), 0.218 (DCC)&nbsp
R-Value Observed:&nbsp0.215&nbsp(Depositor)&nbsp

Space Group:&nbspC 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.62	α = 90
b = 35.87	β = 94.11
c = 75.69	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
Arcimboldo	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View&nbspFull Validation Report

View more in-depth experimental data

Entry History&nbsp

Deposition Data

Released Date:&nbsp2013-09-11&nbsp

Deposition Author(s):&nbsp

De Pereda, J.M.

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2013-09-25
Changes: Database references
Version 1.2: 2013-11-20
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references

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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.