6RLH | pdb_00006rlh

The structure of 3fPizza6-SH obtained via vapour diffusion

PDB DOI: https://doi.org/10.2210/pdb6RLH/pdb

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

Deposited: 2019-05-02 Released: 2020-11-18
Deposition Author(s): Noguchi, H., Voet, A.R.D.
Funding Organization(s): Research Foundation - Flanders

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Self-assembled Pizza proteins

Noguchi, H., Voet, A.R.D.

To be published.

Macromolecule Content

Total Structure Weight: 25.87 kDa
Atom Count: 2,080
Modeled Residue Count: 248
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3fPizza6-SH	A	256	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: 1.50 Å
R-Value Free: 0.215 (Depositor), 0.220 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.954	α = 90
b = 53.264	β = 102.39
c = 43.452	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	G0E4717N, G0F9316N, G051917N

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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.