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- PDB-1mju: 1.22 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mju | |||||||||
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Title | 1.22 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 | |||||||||
![]() | (IMMUNOGLOBULIN MS6-12) x 2 | |||||||||
![]() | IMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
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 | ![]() | 222.6 KB | Display | ![]() |
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PDB format | ![]() | 184.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.5 KB | Display | ![]() |
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Full document | ![]() | 465.3 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 46.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mh5SC ![]() 1mieC ![]() 1mj7C ![]() 1mj8C ![]() 1mjjC S: Starting model for refinement C: citing same article ( |
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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: 24191.900 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: 24373.428 Da / Num. of mol.: 1 / Fragment: Fab fragment, HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Sodium acetate, NaCl, pH 5.0, 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: Nov 9, 2000 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→10 Å / Num. all: 141368 / Num. obs: 141368 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.22→1.24 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.4 / % possible all: 63.3 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 63.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MH5 Resolution: 1.22→10 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.213 / SU ML: 0.028 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.251 Å / Total num. of bins used: 20 /
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.154 / Rfactor Rwork: 0.123 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |