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- PDB-1b4m: NMR STRUCTURE OF APO CELLULAR RETINOL-BINDING PROTEIN II, 24 STRU... -

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Entry
Database: PDB / ID: 1b4m
TitleNMR STRUCTURE OF APO CELLULAR RETINOL-BINDING PROTEIN II, 24 STRUCTURES
ComponentsCELLULAR RETINOL-BINDING PROTEIN II
KeywordsRETINOL TRANSPORT / CELLULAR RETINOL-BINDING PROTEIN / LIPID TRANSPORT / CRBP II / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


Retinoid metabolism and transport / retinal binding / retinol metabolic process / retinol binding / fatty acid transport / retinoid metabolic process / fatty acid binding / lipid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Retinol-binding protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / SIMULATED ANNEALING REFINEMENT
AuthorsLu, J. / Lin, C.-L. / Tang, C. / Ponder, J.W. / Kao, J.L.F. / Cistola, D.P. / Li, E.
Citation
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.
#1: 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.
#2: 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.
#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: 1993
Title: Crystal Structures of Holo and Apo-Cellular Retinol-Binding Protein II
Authors: Winter, N.S. / Bratt, J.M. / Banaszak, L.J.
History
DepositionDec 23, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
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


Theoretical massNumber of molelcules
Total (without water)15,6071
Polymers15,6071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 25FINAL PENALTY FUNCTION VALUES WITHIN 2 STANDARD DEVIATIONS FROM THE MEAN
RepresentativeModel #12

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Components

#1: Protein CELLULAR RETINOL-BINDING PROTEIN II / CRBP 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 / Plasmid: PMON-CRBP II / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P06768

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113-D 15N
12113C-RESOLVED NOESY
NMR detailsText: THE LIMITS ON SECONDARY STRUCTURE ELEMENTS WERE DEFINED BY THE PROTON-CARBON CONSENSUS CHEMICAL SHIFT INDEX.

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionspH: 7.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TinkerPONDERrefinement
Tinkerstructure solution
RefinementMethod: SIMULATED ANNEALING REFINEMENT / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: FINAL PENALTY FUNCTION VALUES WITHIN 2 STANDARD DEVIATIONS FROM THE MEAN
Conformers calculated total number: 25 / Conformers submitted total number: 24

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