3I17 | pdb_00003i17

Crystal structure of the apo R132K:L121E mutant of cellular retinoic acid-binding protein II at 1.68 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb3I17/pdb

• Classification: lipid binding, retinal binding
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-25 Released: 2009-07-28 
• Deposition Author(s): Jia, X., Watson, C.T., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Elucidating the exact role of engineered CRABPII residues for the formation of a retinal protonated Schiff base.

Vasileiou, C., Wang, W., Jia, X., Lee, K.S., Watson, C.T., Geiger, J.H., Borhan, B.

(2009) Proteins 77: 812-822

• PubMed: 19603486 
• DOI: https://doi.org/10.1002/prot.22495
• Primary Citation Related Structures: 
  3I17


• PubMed Abstract: 
  

  Cellular Retinoic Acid Binding Protein II (CRABPII) has been reengineered to specifically bind and react with all-trans-retinal to form a protonated Schiff base. Each step of this process has been dissected and four residues (Lys132, Tyr134, Arg111, and Glu121) within the CRABPII binding site have been identified as crucial for imine formation and/or protonation. The precise role of each residue has been examined through site directed mutagenesis and crystallographic studies. The crystal structure of the R132K:L121E-CRABPII (PDB-3I17) double mutant suggests a direct interaction between engineered Glu121 and the native Arg111, which is critical for both Schiff base formation and protonation.

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Organizational Affiliation: 
• Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.14 kDa 
• Atom Count: 2,455 
• Modeled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular retinoic acid-binding protein 2	A [auth B], B [auth A]	137	Homo sapiens	Mutation(s): 2  Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens) Explore P29373  Go to UniProtKB:  P29373
PHAROS:  P29373 GTEx:  ENSG00000143320

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.699	α = 105.8
b = 37.271	β = 106.44
c = 60.371	γ = 89.97

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Jia, X., Watson, C.T., Geiger, J.H.

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-28
  Changes: Structure summary
• Version 1.3: 2021-10-13
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description