3LYG | pdb_00003lyg

Crystal structure of NTF2-like protein of unknown function (YP_270605.1) from Colwellia psychrerythraea 34H at 1.61 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LYG/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Colwellia psychrerythraea 34H
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-26 Released: 2010-04-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Crystal structure of NTF2-like protein of unknown function (YP_270605.1) from Colwellia psychrerythraea 34H at 1.61 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: 14.12 kDa 
• Atom Count: 1,191 
• Modeled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTF2-like protein of unknown function	A	120	Colwellia psychrerythraea 34H	Mutation(s): 0  Gene Names: CPS_3947
UniProt
Find proteins for Q47X65 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681)) Explore Q47X65  Go to UniProtKB:  Q47X65

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	B [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
UNL	C [auth A]	Unknown ligand RAXXELZNTBOGNW-UHFFFAOYSA-O

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: 1.61 Å
• R-Value Free:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LYG

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.387	α = 90
b = 57.387	β = 90
c = 67.339	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: 2010-04-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary