6PQK | pdb_00006pqk

Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A

PDB DOI: https://doi.org/10.2210/pdb6PQK/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Bacillus amyloliquefaciens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-07-09 Released: 2020-07-15
Deposition Author(s): Caro, J.A., Djanto, V., Wand, A.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.160 (Depositor), 0.162 (DCC)
R-Value Work:
0.138 (Depositor), 0.139 (DCC)
R-Value Observed:
0.138 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6PQK

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

Literature

Targeting conformational entropy to modulate binding affinity

Caro, J.A., Djanto, V., Wand, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 50.35 kDa
Atom Count: 4,014
Modeled Residue Count: 394
Deposited Residue Count: 436
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease	A, B [auth C]	128	Bacillus amyloliquefaciens	Mutation(s): 2 EC: 3.1.27
UniProt
Find proteins for P00648 (Bacillus amyloliquefaciens) Explore P00648 Go to UniProtKB: P00648
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00648
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Barstar	C [auth B], D	90	Bacillus amyloliquefaciens	Mutation(s): 4
UniProt
Find proteins for P11540 (Bacillus amyloliquefaciens) Explore P11540 Go to UniProtKB: P11540
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11540
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	E [auth A], J [auth B], K [auth D], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C]	F [auth A], G [auth A], H [auth C], I [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.160 (Depositor), 0.162 (DCC)
R-Value Work: 0.138 (Depositor), 0.139 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.704	α = 90
b = 68.404	β = 90
c = 166.723	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM102447

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Structure summary

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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.