+Open data
-Basic information
Entry | Database: PDB / ID: 1eii | ||||||
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Title | NMR STRUCTURE OF HOLO CELLULAR RETINOL-BINDING PROTEIN II | ||||||
Components | CELLULAR RETINOL-BINDING PROTEIN II | ||||||
Keywords | TRANSPORT 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 | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Lu, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eii.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1eii.ent.gz | 901.9 KB | Display | PDB format |
PDBx/mmJSON format | 1eii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eii_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 1eii_full_validation.pdf.gz | 701.6 KB | Display | |
Data in XML | 1eii_validation.xml.gz | 111.9 KB | Display | |
Data in CIF | 1eii_validation.cif.gz | 128.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/1eii ftp://data.pdbj.org/pub/pdb/validation_reports/ei/1eii | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-RTL / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: FINAL PENALTY FUNCTION VALUES WITHIN 2 STANDARD DEVIATIONS FROM THE MEAN Conformers calculated total number: 30 / Conformers submitted total number: 25 |