8U5W

De novo designed pentameric helical bundle protein

PDB DOI: https://doi.org/10.2210/pdb8U5W/pdb

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

Deposited: 2023-09-13 Released: 2024-09-25
Deposition Author(s): Bick, M.J., Xu, C., Sankaran, B., Baker, D.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.279
R-Value Work: 0.234
R-Value Observed: 0.238

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

De novo Design of Near Infrared Fluorescent Proteins

Xu, C., Liu, Y., Arus, B.A., Mishra, K., Bandi, V.G., Luciano, M.P., Kumar, A., Manton, J., Guo, Z., Bick, M.J., Xu, M., Zhang, K., Kang, A., De La Cruz, J., Brackenbrough, E., Gerben, S.R., Bera, A.K., Vaughan, J.C., Derivery, E., Schnermann, M.J., Stiel, A.C., Bruns, O., Baker, D.

To be published.

Macromolecule Content

Total Structure Weight: 89.67 kDa
Atom Count: 4,456
Modelled Residue Count: 670
Deposited Residue Count: 740
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WSHC5	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	74	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.279
R-Value Work: 0.234
R-Value Observed: 0.238
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.588	α = 90
b = 74.353	β = 90
c = 194.338	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-09-25
Type: Initial release

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 R01GM133198.