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Yorodumi- PDB-32c2: STRUCTURE OF AN ACTIVITY SUPPRESSING FAB FRAGMENT TO CYTOCHROME P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 32c2 | ||||||
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Title | STRUCTURE OF AN ACTIVITY SUPPRESSING FAB FRAGMENT TO CYTOCHROME P450 AROMATASE | ||||||
Components | (IGG1 ANTIBODY 32C2) x 2 | ||||||
Keywords | IMMUNE SYSTEM / FAB / ANTIBODY / AROMATASE / P450 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Sawicki, M.W. / Ng, P.C. / Burkhart, B. / Pletnev, V. / Higashiyama, T. / Osawa, Y. / Ghosh, D. | ||||||
Citation | Journal: Mol.Immunol. / Year: 1999 Title: Structure of an activity suppressing Fab fragment to cytochrome P450 aromatase: insights into the antibody-antigen interactions. Authors: Sawicki, M.W. / Ng, P.C. / Burkhart, B.M. / Pletnev, V.Z. / Higashiyama, T. / Osawa, Y. / Ghosh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 32c2.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb32c2.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 32c2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/2c/32c2 ftp://data.pdbj.org/pub/pdb/validation_reports/2c/32c2 | HTTPS FTP |
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-Related structure data
Related structure data | 1flrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23827.373 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23468.115 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.4 Details: 0.2M SODIUM ACETATE, PH 4.4 @ 12 MG/ML. PRECIPITANT WAS 25% PEG 3350, pH 4.40 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→99 Å / Num. obs: 9161 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Rsym value: 0.091 |
Reflection shell | Resolution: 3→3.19 Å / % possible all: 71.9 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 99 Å / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Num. measured all: 42185 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.19 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FLR Resolution: 3→99 Å / Rfactor Rfree error: 0.011 / Data cutoff high rms absF: 196784 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 45 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 99 Å / Rfactor obs: 0.2124 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.344 / Rfactor Rwork: 0.264 |