+Open data
-Basic information
Entry | Database: PDB / ID: 1f3d | ||||||
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Title | CATALYTIC ANTIBODY 4B2 IN COMPLEX WITH ITS AMIDINIUM HAPTEN. | ||||||
Components | (CATALYTIC ANTIBODY 4B2) x 2 | ||||||
Keywords | IMMUNE SYSTEM / catalytic antibody / amidinium / haptenic charge | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Golinelli-Pimpaneau, B. / Goncalves, O. / Dintinger, T. / Blanchard, D. / Knossow, M. / Tellier, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Structural evidence for a programmed general base in the active site of a catalytic antibody. Authors: Golinelli-Pimpaneau, B. / Goncalves, O. / Dintinger, T. / Blanchard, D. / Knossow, M. / Tellier, C. #1: Journal: BIOCHEM.J. / Year: 2000 Title: Mechanism of an Antibody-Catalysed Allylic Isomerization. Authors: Goncalves, O. / Dintinger, T. / Lebreton, J. / Blanchard, D. / Tellier, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f3d.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f3d.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 1f3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f3d_validation.pdf.gz | 481.3 KB | Display | wwPDB validaton report |
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Full document | 1f3d_full_validation.pdf.gz | 489.8 KB | Display | |
Data in XML | 1f3d_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 1f3d_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f3d ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f3d | 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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-Components
#1: Antibody | Mass: 24206.977 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN - FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue fraction: ASCITES FLUID / References: UniProt: A2NHM3*PLUS #2: Antibody | Mass: 23292.092 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN - FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue fraction: ASCITES FLUID #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, ammonium sulfate, acetate, stontium chloride, glycerol, dioxan, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9607 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 29, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9607 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→20 Å / Num. all: 81391 / Num. obs: 79647 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 1.84 % / Biso Wilson estimate: 24.15 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3755 / % possible all: 94.9 |
Reflection | *PLUS Num. measured all: 155936 |
Reflection shell | *PLUS % possible obs: 94.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.87→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.198 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.87 Å / Lowest resolution: 1.9 Å / Rfactor Rfree: 0.281 / Rfactor obs: 0.274 |