2RFR

Crystal structure of an ntf2-like protein with a cystatin-like fold (saro_3722) from novosphingobium aromaticivorans dsm at 1.16 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RFR/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-01 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: 1.16 Å
• R-Value Free: 0.172 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Literature

Crystal structure of uncharacterized protein (YP_001166107.1) from Novosphingobium aromaticivorans DSM 12444 at 1.16 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.89 kDa 
• Atom Count: 1,549 
• Modelled Residue Count: 154 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	155	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0  Gene Names: YP_001166107.1, Saro_3722
UniProt
Find proteins for A4XF70 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XF70  Go to UniProtKB:  A4XF70

Small Molecules

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: 1.16 Å
• R-Value Free: 0.172 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 3 2 1
• Diffraction Data: https://doi.org/10.18430/M32RFR

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.135	α = 90
b = 63.135	β = 90
c = 75.118	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction

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: Source and taxonomy, 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