3JR1 | pdb_00003jr1

Crystal structure of Putative fructosamine-3-kinase (YP_719053.1) from HAEMOPHILUS SOMNUS 129PT at 2.32 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3JR1/pdb

• Classification: TRANSFERASE
• Organism(s): Histophilus somni 129PT
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-08 Released: 2009-09-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of Putative fructosamine-3-kinase (YP_719053.1) from HAEMOPHILUS SOMNUS 129PT at 2.32 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 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.24 kDa 
• Atom Count: 5,091 
• Modeled Residue Count: 591 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative fructosamine-3-kinase	A, B	312	Histophilus somni 129PT	Mutation(s): 0  Gene Names: HS_0843, YP_719053.1
UniProt
Find proteins for Q0I3M3 (Histophilus somni (strain 129Pt)) Explore Q0I3M3  Go to UniProtKB:  Q0I3M3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	C [auth A], F [auth B]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33JR1

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.308	α = 90
b = 85.627	β = 132.92
c = 99.009	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary