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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Thermotoga maritima Hfq homolog

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein Hfq	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 ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')	M [auth N], N [auth O]	6	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (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

Entry History 

Deposition Data

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

Revision History  

• 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