2RFF | pdb_00002rff

Crystal structure of a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RFF/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-28 Released: 2007-10-16 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Crystal structure of a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 13.26 kDa 
• Atom Count: 1,105 
• Modeled Residue Count: 111 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative nucleotidyltransferase	A	111	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: NP_343093.1, SSO1673
UniProt
Find proteins for Q97XP0 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97XP0  Go to UniProtKB:  Q97XP0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.40 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32RFF

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.007	α = 77.24
b = 29.884	β = 73.72
c = 35.202	γ = 78.3

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
SOLVE	phasing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary