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Yorodumi- PDB-1jp5: Crystal structure of the single-chain Fv fragment 1696 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jp5 | ||||||
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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-1 protease | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody-antigen complex / HIV PR inhibiting antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Rezacova, P. / Lescar, J. / Brynda, J. / Fabry, M. / Horejsi, M. / Sedlacek, J. / Bentley, G.A. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structural basis of HIV-1 and HIV-2 protease inhibition by a monoclonal antibody. Authors: Rezacova, P. / Lescar, J. / Brynda, J. / Fabry, M. / Horejsi, M. / 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 | 1jp5.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jp5.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 1jp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jp5_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 1jp5_full_validation.pdf.gz | 462.1 KB | Display | |
Data in XML | 1jp5_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1jp5_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/1jp5 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/1jp5 | HTTPS FTP |
-Related structure data
Related structure data | 1cl7S 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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2 |
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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) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) #2: Protein/peptide | Mass: 1199.404 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: octamer PQITLWQR from the N-terminus of HIV-1 protease, R added to the C-terminus to increase solubility #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: 2.09 Å3/Da / Density % sol: 41.07 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.05M tri-sodium citrate, 0.1M sodium phosphate, 24% PEG 3400, 0.2M ammonium sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 292K | ||||||||||||||||||||||||||||||||||||
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: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 12, 2000 |
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: 2.7→30 Å / Num. all: 12910 / Num. obs: 12620 / % possible obs: 96.7 % / Redundancy: 9.6 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.06 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.323 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: variable domains of Fab 1696 (PDB code 1CL7) Resolution: 2.7→19.46 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 897041.43 / 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: 16.6893 Å2 / ksol: 0.317164 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.3 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.385 / % reflection Rfree: 11.2 % / Rfactor Rwork: 0.31 |