6QLB | pdb_00006qlb

Calpain small subunit 1, RNA-binding protein Hfq

PDB DOI: https://doi.org/10.2210/pdb6QLB/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-31 Released: 2020-02-05
Deposition Author(s): Rizkallah, P.J., Cresser-Brown, J.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.247 (Depositor), 0.249 (DCC)
R-Value Work:
0.201 (Depositor), 0.205 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Calpain small subunit 1, RNA-binding protein Hfq

Rizkallah, P.J., Cresser-Brown, J.O.

(2020) Acta Crystallogr Sect F Struct Biol Cryst Commun

Macromolecule Content

Total Structure Weight: 110.04 kDa
Atom Count: 7,880
Modeled Residue Count: 943
Deposited Residue Count: 944
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calpain small subunit 1	A, B, C, D	173	Homo sapiens	Mutation(s): 0 Gene Names: CAPNS1, CAPN4, CAPNS
UniProt & NIH Common Fund Data Resources
Find proteins for P04632 (Homo sapiens) Explore P04632 Go to UniProtKB: P04632
PHAROS: P04632 GTEx: ENSG00000126247
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04632
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein Hfq	E, F, G, H	63	Escherichia coli	Mutation(s): 0 Gene Names: hfq, NCTC13125_02619
UniProt
Find proteins for P0A6X3 (Escherichia coli (strain K12)) Explore P0A6X3 Go to UniProtKB: P0A6X3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4G Query on P4G Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain U [auth B] mmCIF format, chain V [auth C] mmCIF format, chain U [auth B]	U [auth B], V [auth C]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Focus chain V [auth C] Interactions & Density Focus chain U [auth B] Focus chain V [auth C]
GUN Query on GUN Download:Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain HA [auth F] SDF format, chain N [auth A] SDF format, chain IA [auth H] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain IA [auth H] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain IA [auth H]	GA [auth E], HA [auth F], IA [auth H], N [auth A]	GUANINE C₅ H₅ N₅ O UYTPUPDQBNUYGX-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth H] Focus chain N [auth A] Interactions & Density Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth H] Focus chain N [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain I [auth A] SDF format, chain FA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth D]	AA [auth C] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth C], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.247 (Depositor), 0.249 (DCC)
R-Value Work: 0.201 (Depositor), 0.205 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.607	α = 90
b = 147.607	β = 90
c = 147.607	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Rizkallah, P.J.

Cresser-Brown, J.O.

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description