+Open data
-Basic information
Entry | Database: PDB / ID: 2a1l | ||||||
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Title | Rat PITP-Beta Complexed to Phosphatidylcholine | ||||||
Components | Phosphatidylinositol transfer protein beta isoform | ||||||
Keywords | LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information PI and PC transport between ER and Golgi membranes / sphingomyelin transfer activity / phosphatidylcholine transfer activity / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / phosphatidylcholine binding / phospholipid transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phosphatidylinositol binding / in utero embryonic development ...PI and PC transport between ER and Golgi membranes / sphingomyelin transfer activity / phosphatidylcholine transfer activity / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / phosphatidylcholine binding / phospholipid transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phosphatidylinositol binding / in utero embryonic development / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Vordtriede, P.B. / Doan, C.N. / Tremblay, J.M. / Helmkamp, G.M. / Yoder, M.D. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structure of PITPbeta in Complex with Phosphatidylcholine: Comparison of Structure and Lipid Transfer to Other PITP Isoforms. Authors: Vordtriede, P.B. / Doan, C.N. / Tremblay, J.M. / Helmkamp, G.M. / Yoder, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a1l.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a1l.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/2a1l ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a1l | HTTPS FTP |
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-Related structure data
Related structure data | 1t27S 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
#1: Protein | Mass: 31364.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pitpnb / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P53812 |
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#2: Chemical | ChemComp-PCW / |
#3: 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: 2.3 Å3/Da / Density % sol: 46.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 400, SODIUM CHLORIDE, SODIUM Potassium phosphate buffer, pH 6.20, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2004 | |||||||||
Radiation | Monochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.18→32.23 Å / Num. all: 15998 / Num. obs: 15160 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.5 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 39.2 | |||||||||
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.275 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T27, PITP-ALPHA MINUS THE REGULATORY LOOP AND THE PHOSPHOLIPID LIGAND Resolution: 2.18→38.23 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2734959.74 / Data cutoff high rms absF: 2734959.74 / Data cutoff low absF: 0 / 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: 55.9138 Å2 / ksol: 0.368711 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.18→38.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.32 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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