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- PDB-1psk: THE CRYSTAL STRUCTURE OF AN FAB FRAGMENT THAT BINDS TO THE MELANO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1psk | ||||||
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Title | THE CRYSTAL STRUCTURE OF AN FAB FRAGMENT THAT BINDS TO THE MELANOMA-ASSOCIATED GD2 GANGLIOSIDE | ||||||
![]() | (ANTIBODY) x 2 | ||||||
![]() | IMMUNOGLOBULIN / FAB / GD2-GANGLIOSIDE / CARBOHYDRATE / MELANOMA | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pichla, S.L. / Murali, R. / Burnett, R.M. | ||||||
![]() | ![]() Title: The crystal structure of a Fab fragment to the melanoma-associated GD2 ganglioside. Authors: Pichla, S.L. / Murali, R. / Burnett, R.M. #1: ![]() Title: Preliminary Crystallographic Data for an Fab to the Melanoma-Associated Gd2 Ganglioside, and the Purification of a Soluble Form of This Antigen Authors: Pichla, S.L. / Murali, R. / Burnett, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.5 KB | Display | ![]() |
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PDB format | ![]() | 81.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.2 KB | Display | ![]() |
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Full document | ![]() | 384.6 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fbjS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23209.670 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 22368.936 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 30% (W/V) PEG 4000, 1% MPD, TRIS BUFFER, PH 7.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1990 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 14677 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.8→3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.147 / % possible all: 95.4 |
Reflection | *PLUS Num. measured all: 33212 |
Reflection shell | *PLUS % possible obs: 95.4 % / Num. unique obs: 2021 / Num. measured obs: 4012 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2FBJ Resolution: 2.8→8 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.93 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.29 |