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Yorodumi- PDB-1mid: Non-specific lipid transfer protein 1 from barley in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mid | ||||||
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Title | Non-specific lipid transfer protein 1 from barley in complex with L-alfa-lysophosphatidylcholine, Laudoyl | ||||||
Components | nonspecific lipid-transfer protein 1 | ||||||
Keywords | LIPID BINDING PROTEIN / lipid transfer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Hordeum vulgare (barley) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Henriksen, A. | ||||||
Citation | Journal: To be Published Title: Binding of L-alfa-lysophosphatidylcholine, lauroyl in the hydrophobic channel of barley lipid transfer protein Authors: Henriksen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mid.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mid.ent.gz | 20.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/1mid ftp://data.pdbj.org/pub/pdb/validation_reports/mi/1mid | HTTPS FTP |
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-Related structure data
Related structure data | 1mzlS 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: 9704.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Strain: cv.ALEXIS / Tissue: SEEDSSeed / References: UniProt: P07597 | ||
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#2: Chemical | #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: 1.79 Å3/Da / Density % sol: 31.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.1M sodium citrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 2000 / Details: mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→21.93 Å / Num. all: 7578 / Num. obs: 7578 / % possible obs: 96 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.17 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.71→1.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 4.4 / Num. unique all: 693 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MZL Resolution: 1.71→21.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 559390.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The side chains of ARG 56, PRO 83 AND ASP 84 are disordered and have not been included in the model. Some atoms in the LPL ligand had no significant electron density and have been omitted from the model
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.2627 Å2 / ksol: 0.382403 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.71→21.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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