+Open data
-Basic information
Entry | Database: PDB / ID: 1e6o | ||||||
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Title | Crystal structure of Fab13B5 against HIV-1 capsid protein p24 | ||||||
Components |
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Keywords | IMMUNOGLOBULIN / FAB / ANTIBODY / ANTIGEN / HIV-1 / P24 / CA | ||||||
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: 1.8 Å | ||||||
Authors | Monaco-Malbet, S. / Berthet-Colominas, C. / Novelli, A. / Battai, N. / Piga, N. / Mallet, F. / Cusack, S. | ||||||
Citation | Journal: Structure / Year: 2000 Title: Mutual Conformational Adaptations in Antigen and Antibody Upon Complex Formation between an Fab and HIV-1 Capsid Protein P24 Authors: Monaco-Malbet, S. / Berthet-Colominas, C. / Novelli, A. / Battai, N. / Piga, N. / Cheynet, V. / Mallet, F. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e6o.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e6o.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 1e6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/1e6o ftp://data.pdbj.org/pub/pdb/validation_reports/e6/1e6o | HTTPS FTP |
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-Related structure data
Related structure data | 1e6jC 1afvS C: citing same article (ref.) 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: 23552.301 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN 1-219 / Source method: isolated from a natural source / Details: OBTAINED BY PEPSIN CLEAVAGE (FAB') / Source: (natural) MUS MUSCULUS (house mouse) |
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#2: Antibody | Mass: 23285.732 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN 1-210 / Source method: isolated from a natural source / Details: OBTAINED BY PEPSIN CLEAVAGE (FAB') / Source: (natural) MUS MUSCULUS (house mouse) |
#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: 2.2 Å3/Da / Density % sol: 44 % | |||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 7MG/ML OF FAB'13B5 IN 0.1M PIPES PH=7.8 IN 9% TO 11% PEG8000 AFTER EQUILIBRATION IN HANGING DROPS AT 22C, pH 7.80 | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||
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: BM14 / Wavelength: 0.799 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.799 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 35964 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.063 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.5 % / Rsym value: 0.127 / % possible all: 85.4 |
Reflection | *PLUS % possible obs: 94 % / Num. measured all: 124392 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 85.5 % / Rmerge(I) obs: 0.128 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AFV Resolution: 1.8→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 Details: LAST 4 AA OF L CHAIN ARE NOT SEQUENCED BUT PRESUMED TO BE RNEC
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Displacement parameters | Biso mean: 27.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.32 |