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- PDB-1eii: NMR STRUCTURE OF HOLO CELLULAR RETINOL-BINDING PROTEIN II -

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Basic information

Entry
Database: PDB / ID: 1eii
TitleNMR STRUCTURE OF HOLO CELLULAR RETINOL-BINDING PROTEIN II
ComponentsCELLULAR RETINOL-BINDING PROTEIN II
KeywordsTRANSPORT PROTEIN / PROTEIN-LIGAND COMPLEX / BETA BARREL / HELIX-TURN-HELIX
Function / homology
Function and homology information


Retinoid metabolism and transport / retinal binding / retinol metabolic process / retinol binding / fatty acid transport / fatty acid binding / lipid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINOL / Retinol-binding protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLu, J. / Lin, C.L. / Tang, C. / Ponder, J.W. / Kao, J.L. / Cistola, D.P. / Li, E.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics.
Authors: Lu, J. / Lin, C.L. / Tang, C. / Ponder, J.W. / Kao, J.L. / Cistola, D.P. / Li, E.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The Structure and Dynamics of Rat Apo-Cellular Retinol-Binding Protein II in Solution: Comparison with the X-ray Structure
Authors: Lu, J. / Lin, C.L. / Tang, C. / Ponder, J.W. / Kao, J.L. / Cistola, D.P. / Li, E.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structures of Holo and Apo-Cellular Retinol-Binding Protein II
Authors: Winter, N.S. / Bratt, J.M. / Banaszak, L.J.
#3: Journal: ADV.PROTEIN CHEM. / Year: 1994
Title: Lipid-Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins
Authors: Banaszak, L. / Winter, N. / Xu, Z. / Bernlohr, D.A. / Cowan, S. / Jones, T.A.
#4: Journal: J.Mol.Biol. / Year: 1996
Title: The NMR Solution Structure of Intestinal Fatty Acid-Binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm
Authors: Hodsdon, M.E. / Ponder, J.W. / Cistola, D.P.
#5: Journal: Biochemistry / Year: 1997
Title: Ligand Binding Alters the Backbone Mobility of Intestinal Fatty Acid-Binding Protein as Monitored by 15N NMR Relaxation and 1H Exchange
Authors: Hodsdon, M.E. / Cistola, D.P.
History
DepositionFeb 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLULAR RETINOL-BINDING PROTEIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8932
Polymers15,6071
Non-polymers2861
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 30FINAL PENALTY FUNCTION VALUES WITHIN 2 STANDARD DEVIATIONS FROM THE MEAN
RepresentativeModel #2closest to the average

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Components

#1: Protein CELLULAR RETINOL-BINDING PROTEIN II / CRBP-II


Mass: 15606.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: SMALL INTESTINAL ENTEROCYTE / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P06768
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1312D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM CELLULAR RETINOL-BINDING PROTEIN II U-15N,13C, complexed with all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer95% H2O/5% D2O
21.5 mM CELLULAR RETINOL-BINDING PROTEIN II U-15N,13C, complexed with all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer99% D2O
31.5 mM CELLULAR RETINOL-BINDING PROTEIN II U-15N, complexed with all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer95% H2O/5% D2O
40.2 mM CELLULAR RETINOL-BINDING PROTEIN II natural abundance, complexed with (2,3,6,7,8,9,10,11,19-13C)-all-trans retinol in 1-to-1 molar ratio; 20 mM phosphate buffer99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.081 7.4 ambient 298 K
20.079 6.5 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
Tinker3.3Ponderstructure solution
Tinker3.3Ponderrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structure calculations were carried out using TINKER, a software package for molecular mechanics and dynamics. The protocol employs metric matrix distance geometry with pairwise Gaussian ...Details: The structure calculations were carried out using TINKER, a software package for molecular mechanics and dynamics. The protocol employs metric matrix distance geometry with pairwise Gaussian metrization followed by simulated annealing. The unique distance geometry algorithm implemented in TINKER overcomes the sampling and scaling problems of earlier distance geometry methods and is computationally more efficient.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: FINAL PENALTY FUNCTION VALUES WITHIN 2 STANDARD DEVIATIONS FROM THE MEAN
Conformers calculated total number: 30 / Conformers submitted total number: 25

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