3FF2 | pdb_00003ff2

Crystal structure of an uncharacterized cystatin fold protein (saro_2299) from novosphingobium aromaticivorans dsm at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3FF2/pdb

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


• Deposited: 2008-12-01 Released: 2008-12-16 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal structure of uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily (YP_497570.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 13.15 kDa 
• Atom Count: 1,150 
• Modeled Residue Count: 117 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily	A	117	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0  Gene Names: Saro_2299, YP_497570.1
UniProt
Find proteins for Q2G5Y7 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2G5Y7  Go to UniProtKB:  Q2G5Y7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33FF2

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.86	α = 90
b = 47.86	β = 90
c = 160.023	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-16 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-12-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Structure summary