3AF6 | pdb_00003af6

The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog

• PDB DOI: https://doi.org/10.2210/pdb3AF6/pdb
• NAKB: 3AF6

• Classification: HYDROLASE/RNA
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-24 Released: 2010-04-21 
• Deposition Author(s): Nishida, Y., Ishikawa, H., Nakagawa, N., Masui, R., Kuramitsu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.258 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii

Nishida, Y., Ishikawa, H., Baba, S., Nakagawa, N., Kuramitsu, S., Masui, R.

(2010) Proteins 78: 2395-2398

• PubMed: 20544974 
• DOI: https://doi.org/10.1002/prot.22748
• Primary Citation Related Structures: 
  3AF5, 3AF6

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Organizational Affiliation: 
• Graduate School of Frontier Biological Sciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.44 kDa 
• Atom Count: 5,269 
• Modeled Residue Count: 645 
• Deposited Residue Count: 663 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH1404	A	651	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH1404 EC: 3.1
UniProt
Find proteins for O50112 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O50112  Go to UniProtKB:  O50112

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3'	B, C	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.258 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.438	α = 90
b = 86.438	β = 90
c = 237.501	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Nishida, Y., Ishikawa, H., Nakagawa, N., Masui, R., Kuramitsu, S.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description