6NEK | pdb_00006nek

Crystal structure of a consensus PDZ domain

PDB DOI: https://doi.org/10.2210/pdb6NEK/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-17 Released: 2019-12-25
Deposition Author(s): Sun, Y.J., Gakhar, L., Fuentes, E.J.
Funding Organization(s): American Heart Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.226 (Depositor), 0.242 (DCC)
R-Value Work:
0.197 (Depositor), 0.207 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6NEK

This is version 1.1 of the entry. See complete history.

Literature

Consensus PDZ domain

Sun, Y.J., Sternke, M., Barrick, D., Fuentes, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 9.94 kDa
Atom Count: 704
Modeled Residue Count: 86
Deposited Residue Count: 93
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Consensus PDZ domain	A	93	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.226 (Depositor), 0.242 (DCC)
R-Value Work: 0.197 (Depositor), 0.207 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.62	α = 90
b = 60.09	β = 90
c = 73.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
pointless	data scaling
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

Funding Organization	Location	Grant Number
American Heart Association	United States	15GRNT25740021

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2023-10-11
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.