8P9M | pdb_00008p9m

Hexameric Hfq from Chromobacterium haemolyticum

PDB DOI: https://doi.org/10.2210/pdb8P9M/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Chromobacterium haemolyticum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-06 Released: 2024-05-15
Deposition Author(s): Nikulin, A.D., Lekontseva, N.V.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.281 (Depositor), 0.280 (DCC)
R-Value Work:
0.222 (Depositor), 0.220 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The Structure of the Hfq Protein from Chromobacterium haemolyticum Revealed a New Variant of Regulation of RNA Binding with the Protein

Lekontseva, N.V., Nikulin, A.D.

(2023) Crystallogr Rep 68: 905-911

DOI: https://doi.org/10.1134/S1063774523600928

Macromolecule Content

Total Structure Weight: 58.23 kDa
Atom Count: 3,534
Modeled Residue Count: 410
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein Hfq	A, B, C, D, E A, B, C, D, E, F	85	Chromobacterium haemolyticum	Mutation(s): 0 Gene Names: hfq, B0T39_13335, B0T45_12055, CH06BL_33310, DBB33_18715
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
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.281 (Depositor), 0.280 (DCC)
R-Value Work: 0.222 (Depositor), 0.220 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.505	α = 90
b = 71.653	β = 90
c = 96.652	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Lekontseva, N.V.

Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	--

Revision History (Full details and data files)

Version 1.0: 2024-05-15
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.