+Open data
-Basic information
Entry | Database: PDB / ID: 1lpj | ||||||
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Title | Human cRBP IV | ||||||
Components | Retinol-binding protein IV, cellular | ||||||
Keywords | TRANSPORT PROTEIN / cellular retinol-binding protein / cRBP / retinol / vitamin A / iLBPs | ||||||
Function / homology | Function and homology information retinal binding / retinol binding / fatty acid transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Calderone, V. / Zanotti, G. / Berni, R. / Folli, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Ligand binding and structural analysis of a human putative cellular retinol-binding protein Authors: Folli, C. / Calderone, V. / Ramazzina, I. / Zanotti, G. / Berni, R. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding ...Title: Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding protein in complex with all-trans-retinol. Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A. #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: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Identification, Retinoid Binding and X-Ray Analysis of a Human Retinol-Binding Protein Authors: Folli, C. / Calderone, V. / Ottonello, S. / Bolchi, A. / Zanotti, G. / Stoppini, M. / Berni, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lpj.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpj.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpj ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpj | HTTPS FTP |
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-Related structure data
Related structure data | 1crbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15427.511 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96R05 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.86 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10% PEG 4000, 10% isopropanol, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.606 Å / Num. all: 7611 / Num. obs: 7611 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.3 / Num. unique all: 932 / Rsym value: 0.124 / % possible all: 87.8 |
Reflection | *PLUS Lowest resolution: 28.6 Å / Num. measured all: 19128 |
Reflection shell | *PLUS Lowest resolution: 2.11 Å / % possible obs: 91.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CRB Resolution: 2→24.44 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 112.525 Å2 / ksol: 0.422063 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.17 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.234 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.11 Å / Rfactor Rfree: 0.3 / Num. reflection Rfree: 136 |