4GDO

Structure of a fragment of the rod domain of plectin

PDB DOI: https://doi.org/10.2210/pdb4GDO/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-01 Released: 2013-09-11
Deposition Author(s): De Pereda, J.M., Buey, R.M., Uson, I., Sammito, M.D., De Marino, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

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

Literature

Exploiting tertiary structure through local folds for crystallographic phasing.

Sammito, M., Millan, C., Rodriguez, D.D., de Ilarduya, I.M., Meindl, K., De Marino, I., Petrillo, G., Buey, R.M., de Pereda, J.M., Zeth, K., Sheldrick, G.M., Uson, I.

(2013) Nat Methods 10: 1099-1101

PubMed: 24037245 Search on PubMed
DOI: https://doi.org/10.1038/nmeth.2644
Primary Citation of Related Structures:
4GDO, 4GN0

PubMed Abstract:
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

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Gene Names: PLEC, PLEC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15149 (Homo sapiens) Explore Q15149 Go to UniProtKB: Q15149
PHAROS: Q15149 GTEx: ENSG00000178209
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15149
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: C 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 Full Validation Report

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.