3F7W

Crystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3F7W/pdb
• Entry: 3F7W supersedes: 3D1U

• Classification: TRANSFERASE
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-10 Released: 2008-11-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Crystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.29 kDa 
• Atom Count: 2,752 
• Modelled Residue Count: 288 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative fructosamine-3-kinase	A	288	Thermobifida fusca YX	Mutation(s): 0  Gene Names: Tfu_2340, YP_290396.1
UniProt
Find proteins for Q47ME9 (Thermobifida fusca (strain YX)) Explore Q47ME9  Go to UniProtKB:  Q47ME9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	B [auth A]	Unknown ligand VEXZGXHMUGYJMC-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: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33F7W

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.178	α = 90
b = 91.178	β = 90
c = 82.049	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: 2008-11-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 3D1U

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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