[English] 日本語
Yorodumi- PDB-1h3p: STRUCTURAL CHARACTERISATION OF A MONOCLONAL ANTIBODY SPECIFIC FOR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h3p | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURAL CHARACTERISATION OF A MONOCLONAL ANTIBODY SPECIFIC FOR THE PRES1 REGION OF THE HEPATITIS B VIRUS | |||||||||
Components | (ANTIBODY FAB FRAGMENT) x 2 | |||||||||
Keywords | IMMUNOGLOBULIN / ANTIBODY FAB FRAGMENT | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Pizarro, J.C. / Vulliez-Le-normand, B. / Riottot, M.M. / Budkowska, A. / Bentley, G.A. | |||||||||
Citation | Journal: FEBS Lett. / Year: 2001 Title: Structural and Functional Characterisation of a Monoclonal Antibody Specific for the Pres1 Region of Hepatitis B Virus Authors: Pizarro, J.C. / Vulliez-Le-Normand, B. / Riottot, M.M. / Budkowska, A. / Bentley, G.A. | |||||||||
History |
| |||||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1h3p.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1h3p.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/1h3p ftp://data.pdbj.org/pub/pdb/validation_reports/h3/1h3p | HTTPS FTP |
---|
-Related structure data
Related structure data | 1h1lS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | THE DIMER IS A HETERODIMER FORMED BY ONE FAB LIGHTCHAIN AND ONE FAB HEAVY CHAIN. |
-Components
#1: Antibody | Mass: 23505.330 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 5A19 HYBRIDOME / Strain: BALB/C / References: UniProt: Q65ZL8*PLUS |
---|---|
#2: Antibody | Mass: 26305.312 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 5A19 HYBRIDOME / Strain: BALB/C / References: UniProt: Q52L64*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 Details: 0.1M CYSTEINE, 15% PEG6000, 110MM MGCL2, 60MM TRISHCL PH8.5, 15% GLYCEROL, pH 8.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. obs: 14823 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 6 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 5.6 / % possible all: 88 |
Reflection | *PLUS Lowest resolution: 15 Å / Rmerge(I) obs: 0.077 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1L Resolution: 2.6→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUE NUMBERING FOLLOWS THE KABAT CONVENTION (E.A.KABAT,T.T.WU, M.REID-MILLER, H.M.PERRY, A K.S.GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGIC INTEREST, 5TH ED., NATIONAL INSTITUTES ...Details: RESIDUE NUMBERING FOLLOWS THE KABAT CONVENTION (E.A.KABAT,T.T.WU, M.REID-MILLER, H.M.PERRY, A K.S.GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGIC INTEREST, 5TH ED., NATIONAL INSTITUTES OF HEALTH BETHESDA RESIDUES H129-H132 AND THE LAST TWO RESIDUES OF BOTH HEAVY AND LIGHT CHAINS WERE MODELLED USING STEREOCHEMICAL RESTRAINTS ONLY. RESIDUE H98 HAS MULTIPLE CONFORMATIONS. RESIDUES WITH WEAK DENSITY INDICATION HAVE 0 OCCUPANCY. THESE RESIDUES HAVE BEEN LISTED IN REMARK 465 AND REMARK 470
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.69 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|