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- PDB-1kgl: Solution structure of cellular retinol binding protein type-I in ... -

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Basic information

Entry
Database: PDB / ID: 1kgl
TitleSolution structure of cellular retinol binding protein type-I in complex with all-trans-retinol
ComponentsCELLULAR RETINOL-BINDING PROTEIN TYPE I
KeywordsLIPID BINDING PROTEIN / BETA BARREL / RETINOID CARRIER / HOLO FORM / NMR SPECTROSCOPY / 15N ISOTOPE ENRICHMENT
Function / homology
Function and homology information


regulation of granulocyte differentiation / response to benzoic acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / all-trans-retinol binding / retinoic acid biosynthetic process / maintenance of location in cell / vitamin A metabolic process / lipid storage / retinal binding ...regulation of granulocyte differentiation / response to benzoic acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / all-trans-retinol binding / retinoic acid biosynthetic process / maintenance of location in cell / vitamin A metabolic process / lipid storage / retinal binding / response to vitamin A / retinoic acid metabolic process / retinol metabolic process / retinol binding / lipid homeostasis / response to retinoic acid / fatty acid transport / retinoid metabolic process / lipid droplet / fatty acid binding / cell body / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / 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 / Retinol-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, ENERGY MINIMIZATION
AuthorsFranzoni, L. / Luecke, C. / Perez, C. / Cavazzini, D. / Rademacher, M. / Ludwig, C. / Spisni, A. / Rossi, G.L. / Rueterjans, H.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structure and Backbone Dynamics of Apo- and Holo-cellular Retinol-binding Protein in Solution.
Authors: Franzoni, L. / Lucke, C. / Perez, C. / Cavazzini, D. / Rademacher, M. / Ludwig, C. / Spisni, A. / Rossi, G.L. / Ruterjans, H.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic Studies on a Family of Cellular Lipophilic Transport Proteins
Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A.
History
DepositionNov 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1432
Polymers15,8561
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)20 / 100target function
Representative

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Components

#1: Protein CELLULAR RETINOL-BINDING PROTEIN TYPE I / CRBP-I


Mass: 15856.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RBP-1 / Plasmid: PET11B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02696
#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
1112D TOCSY
1212D NOESY
1312D 15N-HSQC
1412D 15N-HTQC
1513D 15N-TOCSY-HSQC
1613D 15N-NOESY-HSQC

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Sample preparation

DetailsContents: 1.8MM CRBP-I PHOSPHATE BUFFER; 0.05% SODIUM AZIDE
Sample conditionsIonic strength: 20mM POTASSIUM PHOSPHATE / pH: 6 / Pressure: AMBIENT / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover97MSIrefinement
XwinNMR1.3structure solution
AURELIA2.5.9structure solution
Felix97structure solution
nmr2st2.05structure solution
DYANA1.5structure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, ENERGY MINIMIZATION
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2826 NOE-DERIVED DISTANCE RESTRAINTS
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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