+Open data
-Basic information
Entry | Database: PDB / ID: 1lri | ||||||
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Title | BETA-CRYPTOGEIN-CHOLESTEROL COMPLEX | ||||||
Components | Beta-elicitin cryptogein | ||||||
Keywords | TOXIN / cryptogein / cholesterol / sterol carrier protein | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host defense-related programmed cell death / symbiont-mediated killing of host cell / extracellular region Similarity search - Function | ||||||
Biological species | Phytophthora cryptogea (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å | ||||||
Authors | Lascombe, M.-B. / Ponchet, M. / Venard, P. / Milat, M.-L. / Blein, J.-P. / Prange, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: The 1.45 A resolution structure of the cryptogein-cholesterol complex: a close-up view of a sterol carrier protein (SCP) active site. Authors: Lascombe, M.B. / Ponchet, M. / Venard, P. / Milat, M.L. / Blein, J.P. / Prange, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lri.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lri.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lri ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lri | HTTPS FTP |
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-Related structure data
Related structure data | 1bxmS 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: 10326.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytophthora cryptogea (eukaryote) / References: UniProt: P15570 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-CLR / |
#4: 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: 1.92 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium chloride, cholesterol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal grow | *PLUS |
Components of the solutions | *PLUS Conc.: 4.5 M / Chemical formula: NaCl |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 / Wavelength: 0.964 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2001 / Details: FOCUSING MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→9.6 Å / Num. obs: 17432 / % possible obs: 99.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 6 / Redundancy: 3.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.39 / Rsym value: 0.41 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.448→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1084 / Rsym value: 0.144 / % possible all: 97.3 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 64233 |
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1BXM Resolution: 1.45→9.6 Å / Num. parameters: 7573 / Num. restraintsaints: 9191 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: FULL ANISOTROPIC REFINEMENT EXCEPT IN DiSORDERED RESIDUES
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 747.23 / Occupancy sum non hydrogen: 841.24 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→9.6 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection Rfree: 992 / % reflection Rfree: 8 % / Rfactor all: 0.13 / Rfactor Rfree: 0.168 | ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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