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Yorodumi- PDB-1fh5: CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MONOCLONAL ANTIBODY MAK33 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fh5 | ||||||
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Title | CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MONOCLONAL ANTIBODY MAK33 | ||||||
Components | (MONOCLONAL ANTIBODY MAK33) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Fab / BiP | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Augustine, J.G. / de la Calle, A. / Knarr, G. / Buchner, J. / Frederick, C.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The crystal structure of the fab fragment of the monoclonal antibody MAK33. Implications for folding and interaction with the chaperone bip. Authors: Augustine, J.G. / de La Calle, A. / Knarr, G. / Buchner, J. / Frederick, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fh5.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fh5.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fh5_validation.pdf.gz | 412 KB | Display | wwPDB validaton report |
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Full document | 1fh5_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 1fh5_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1fh5_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/1fh5 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/1fh5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Antibody | Mass: 23474.762 Da / Num. of mol.: 1 / Fragment: FAB LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 21460.160 Da / Num. of mol.: 1 / Fragment: FAB HEAVY CHAIN / 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.58 Å3/Da / Density % sol: 77.94 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: na citrate, 16% PEG 8k, 16% glycerol 1.0 M NaCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 53 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 1997 |
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→25 Å / Num. all: 21497 / Num. obs: 20143 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10 |
Reflection shell | Highest resolution: 2.9 Å / Rmerge(I) obs: 0.279 |
Reflection shell | *PLUS % possible obs: 87.1 % / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Resolution: 2.9→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||
Refinement | *PLUS Num. reflection all: 18312 / % reflection Rfree: 8 % | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.014 | ||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 2.97 Å / Rfactor Rfree: 0.329 / Rfactor Rwork: 0.281 |