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- PDB-1mj7: Crystal Structure Of The Complex Of The Fab fragment of Esterolyt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mj7 | ||||||
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Title | Crystal Structure Of The Complex Of The Fab fragment of Esterolytic Antibody MS5-393 and A Transition-State Analog | ||||||
![]() | (IMMUNOGLOBULIN MS5-393) x 2 | ||||||
![]() | IMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN / TSA | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HAL![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. ...Ruzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W. | ||||||
![]() | ![]() Title: High-resolution crystal structure of the Fab-fragments of a family of mouse catalytic antibodies with esterase activity Authors: Ruzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W. #1: ![]() Title: The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue Authors: Muranova, T.A. / Ruzheinikov, S.N. / Sedelnikova, S.E. / Moir, A. / Partridge, L.J. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W. | ||||||
History |
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Remark 999 | sequence an appropriate sequence database reference was not available at the time of processing. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.5 KB | Display | ![]() |
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PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.4 KB | Display | ![]() |
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Full document | ![]() | 733.9 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mh5SC ![]() 1mieC ![]() 1mj8C ![]() 1mjjC ![]() 1mjuC C: citing same article ( 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 24250.902 Da / Num. of mol.: 1 / Fragment: Fab fragment, LIGHT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 24487.488 Da / Num. of mol.: 1 / Fragment: Fab fragment, HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-HAL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, potassium thiocyanate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2001 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→10 Å / Num. all: 17206 / Num. obs: 17206 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.25→2.3 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / % possible all: 84.8 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 84.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1MH5 Resolution: 2.25→10 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.5 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |