6BZX | pdb_00006bzx

Structure of the artificial complex alpha-Rep/Octarellin V.1 crystallized by counter diffusion in a capillary

PDB DOI: https://doi.org/10.2210/pdb6BZX/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-12-26 Released: 2019-01-09
Deposition Author(s): Aedo, F., Contreras-Martel, C., Martinez-Oyanedel, J., Bunster, M., Minard, P., Van de Weerdt, C., Figueroa, M.
Funding Organization(s): Universidad de Concepcion

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.304 (Depositor), 0.300 (DCC)
R-Value Work:
0.245 (Depositor), 0.240 (DCC)
R-Value Observed:
0.251 (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

Crystallization of the artificial complex alpha-Rep/Octarellin V.1 by counter diffusion allowed to have a most complete structure

Aedo, F., Figueroa, M.

To be published.

Macromolecule Content

Total Structure Weight: 57.25 kDa
Atom Count: 3,716
Modeled Residue Count: 475
Deposited Residue Count: 511
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-Rep	A	294	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Octarellin V.1	B	217	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.304 (Depositor), 0.300 (DCC)
R-Value Work: 0.245 (Depositor), 0.240 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.562	α = 90
b = 41.108	β = 106.57
c = 81.409	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-01-09

Deposition Author(s):

Contreras-Martel, C.

Martinez-Oyanedel, J.

Van de Weerdt, C.

Funding Organization	Location	Grant Number
Universidad de Concepcion	Chile	VRID 217.037.023-1.OIN

Revision History (Full details and data files)

Version 1.0: 2019-01-09
Type: Initial release
Version 1.1: 2023-10-04
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.