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Yorodumi- PDB-1svz: Crystal structure of the single-chain Fv fragment 1696 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1svz | ||||||
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Title | Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody-antigen complex / HIV inhibiting antibody | ||||||
Function / homology | Function and homology information immunoglobulin complex / antigen binding / adaptive immune response / immune response / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Rezacova, P. / Brynda, J. / Lescar, J. / Bentley, G.A. / Fabry, M. / Horejsi, M. / Sedlacek, J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2005 Title: Crystal structure of a cross-reaction complex between an anti-HIV-1 protease antibody and an HIV-2 protease peptide Authors: Rezacova, P. / Brynda, J. / Lescar, J. / Fabry, M. / Horejsi, M. / Sieglova, I. / Sedlacek, J. / Bentley, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1svz.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1svz.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 1svz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/1svz ftp://data.pdbj.org/pub/pdb/validation_reports/sv/1svz | HTTPS FTP |
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-Related structure data
Related structure data | 1jp5S 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: Antibody | Mass: 26876.650 Da / Num. of mol.: 2 / Fragment: scFv1696 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Description: T7 promoter-driven plasmid, inclusion bodies production followed by protein in vitro refolding Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01631 #2: Protein/peptide | Mass: 1063.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: octapeptide PQFSLWKR #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: protein concentration 14mg/ml, 0.05M tri-sodium citrate, 0.1M sodium phosphate, 27% PEG 3400, 0.2M ammonium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 14, 2001 |
Radiation | Monochromator: sagitally focused Ge / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→30 Å / Num. all: 35996 / Num. obs: 34737 / % possible obs: 96.5 % / Redundancy: 8.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.88 |
Reflection shell | Resolution: 1.88→1.99 Å / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.5 / % possible all: 77.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JP5 Resolution: 1.89→19.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1358407.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.3367 Å2 / ksol: 0.351579 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.89→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→2 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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