4Y91 | pdb_00004y91

Crystal Structure of a Thermotoga maritima Hfq homolog

PDB DOI: https://doi.org/10.2210/pdb4Y91/pdb
NAKB: 4Y91

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Thermotoga maritima MSB8, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-16 Released: 2016-03-16
Deposition Author(s): Randolph, P.S., Patterson, J., Mura, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.246 (Depositor), 0.248 (DCC)
R-Value Work:
0.184 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4Y91

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of a Thermotoga maritima Hfq homolog

Patterson, J., Randolph, P.S., Mura, C.

To be published.

Macromolecule Content

Total Structure Weight: 133.31 kDa
Atom Count: 6,777
Modeled Residue Count: 809
Deposited Residue Count: 1,152
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

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, G, H, I, J, K, L	95	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: hfq, TM_0526
UniProt
Find proteins for Q9WYZ6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYZ6 Go to UniProtKB: Q9WYZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYZ6
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (5'-R(PUPUPUPUPUPU)-3')	M [auth N], N [auth O]	6	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.246 (Depositor), 0.248 (DCC)
R-Value Work: 0.184 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.08	α = 90
b = 133.5	β = 90
c = 206.18	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-16
Type: Initial release
Version 1.1: 2017-10-11
Changes: Advisory, Data collection, Derived calculations, Experimental preparation
Version 1.2: 2023-09-27
Changes: Advisory, Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.