3QGZ | pdb_00003qgz

Re-investigated high resolution crystal structure of histidine triad nucleotide-binding protein 1 (HINT1) from rabbit complexed with adenosine

• PDB DOI: https://doi.org/10.2210/pdb3QGZ/pdb
• Entry: 3QGZ supersedes: 3LLJ

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-01-25 Released: 2011-02-16 
• Deposition Author(s): Dolot, R.M., Ozga, M., Krakowiak, A., Nawrot, B., Stec, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.168 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

High-resolution X-ray crystal structure of rabbit histidine triad nucleotide-binding protein 1 (rHINT1) - adenosine complex at 1.10A resolution

Dolot, R., Ozga, M., Krakowiak, A., Nawrot, B.

(2011) Acta Crystallogr D Biol Crystallogr 67: 601-607

• PubMed: 21697598 
• DOI: https://doi.org/10.1107/S0907444911015605
• Primary Citation Related Structures: 
  3QGZ


• PubMed Abstract: 
  

  Histidine triad nucleotide-binding protein 1 (HINT1) represents the most ancient and widespread branch in the histidine-triad protein superfamily. HINT1 plays an important role in various biological processes and has been found in many species. Here, the first complete structure of the rabbit HINT1-adenosine complex is reported at 1.10 Å resolution, which is one of the highest resolutions obtained for a HINT1 structure. The final structure has an R(cryst) of 14.25% (R(free) = 16.77%) and the model exhibits good stereochemical qualities. A detailed analysis of the atomic resolution data allowed an update of the details of the protein structure in comparison to previously published data.

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Organizational Affiliation: 
• Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies of the Polish Academy of Sciences, Łódź, Poland. [e-mail]

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: 13.98 kDa 
• Atom Count: 1,204 
• Modeled Residue Count: 114 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 1	A	126	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: HINT1, HINT EC: 3 (PDB Primary Data), 3.4.22 (UniProt), 3.9.1 (UniProt)
UniProt
Find proteins for P80912 (Oryctolagus cuniculus) Explore P80912  Go to UniProtKB:  P80912

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	B [auth A]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.168 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.747	α = 90
b = 39.747	β = 90
c = 141.83	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-16 
Deposition Author(s): Dolot, R.M., Ozga, M., Krakowiak, A., Nawrot, B., Stec, W.J.
• This entry supersedes: 3LLJ

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-26
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Data collection, Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description