5YH1 | pdb_00005yh1

Member of s1p family of ribosomal proteins PF0399 DHH domain

• PDB DOI: https://doi.org/10.2210/pdb5YH1/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-27 Released: 2018-08-01 
• Deposition Author(s): Song, Y., Liu, X.P.
• Funding Organization(s): the National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Member of s1p family of ribosomal proteins PF0399 DHH domain

Song, Y., Liu, X.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.1 kDa 
• Atom Count: 3,687 
• Modeled Residue Count: 439 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Member of s1p family of ribosomal proteins	A	441	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0399
UniProt
Find proteins for Q8U3Q7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3Q7  Go to UniProtKB:  Q8U3Q7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.5	α = 90
b = 132.5	β = 90
c = 212.245	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
AutoSol	phasing
HKL-3000	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Song, Y., Liu, X.P.

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Funding Organization	Location	Grant Number
the National Natural Science Foundation of China	China	31371260

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary