3FSD | pdb_00003fsd

Crystal structure of NTF2-like protein of unknown function in nutrient uptake (YP_427473.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3FSD/pdb

• Classification: structural genomics, unknown function
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-09 Released: 2009-02-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal structure of NTF2-like protein of unknown function in nutrient uptake (YP_427473.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.70 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)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 14.74 kDa 
• Atom Count: 1,054 
• Modeled Residue Count: 121 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTF2-like protein of unknown function in nutrient uptake	A	134	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: Rru_A2386, YP_427473.1
UniProt
Find proteins for Q2RRQ9 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RRQ9  Go to UniProtKB:  Q2RRQ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	B [auth A]	Unknown ligand 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: 1.70 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33FSD

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.018	α = 90
b = 61.018	β = 90
c = 56.442	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: 2009-02-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2016-02-17
  Changes: Refinement description
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.7: 2024-10-30
  Changes: Data collection, Structure summary