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- PDB-1mh5: The Structure Of The Complex Of The Fab Fragment Of The Esterolyt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mh5 | ||||||
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Title | The Structure Of The Complex Of The Fab Fragment Of The Esterolytic Antibody MS6-164 and A Transition-State Analog | ||||||
![]() | (IMMUNOGLOBULIN MS6-164) x 2 | ||||||
![]() | IMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN | ||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
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 | ![]() | 174 KB | Display | ![]() |
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PDB format | ![]() | 142.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 975 KB | Display | ![]() |
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Full document | ![]() | 1008.5 KB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 56.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mieC ![]() 1mj7C ![]() 1mj8C ![]() 1mjjC ![]() 1mjuC ![]() 1a3lS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 24181.863 Da / Num. of mol.: 2 / Fragment: Fab fragment, LIGHT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 24853.977 Da / Num. of mol.: 2 / Fragment: Fab fragment, HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.9 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 3.3 Details: PEG 8000, LITIUM SULPHATE, ACETIC ACID, pH 3.3, 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 5, 2000 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.244 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→10 Å / Num. all: 51508 / Num. obs: 51508 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2 / % possible all: 47.5 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 47.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A3L Resolution: 2.1→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 54 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |