+Open data
-Basic information
Entry | Database: PDB / ID: 35c8 | ||||||
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Title | CATALYTIC ANTIBODY 5C8, FAB-INHIBITOR COMPLEX | ||||||
Components | (IGG 5C8) x 2 | ||||||
Keywords | CATALYTIC ANTIBODY / FAB / RING CLOSURE REACTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gruber, K. / Wilson, I.A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural basis for antibody catalysis of a disfavored ring closure reaction. Authors: Gruber, K. / Zhou, B. / Houk, K.N. / Lerner, R.A. / Shevlin, C.G. / Wilson, I.A. #1: Journal: To be Published Title: Ligand-Induced Conformational Changes in a Catalytic Antibody: Comparison of the Bound and Unbound Structure of Fab 5C8 Authors: Gruber, K. / Heine, A. / Stura, E.A. / Shevlin, C.G. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 35c8.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb35c8.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 35c8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 35c8_validation.pdf.gz | 662.3 KB | Display | wwPDB validaton report |
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Full document | 35c8_full_validation.pdf.gz | 668.4 KB | Display | |
Data in XML | 35c8_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 35c8_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/5c/35c8 ftp://data.pdbj.org/pub/pdb/validation_reports/5c/35c8 | HTTPS FTP |
-Related 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: 23148.482 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: EMBL: X79906, UniProt: P01837*PLUS |
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#2: Antibody | Mass: 23097.658 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: PIR: S49220 |
#3: Chemical | ChemComp-NOX / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: PT COATED FUSED SILICA |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 33264 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.065 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2→2.03 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.387 / % possible all: 97.6 |
Reflection | *PLUS Num. measured all: 249541 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.387 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FREE FAB 5C8 Resolution: 2→50 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 23.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.206 / Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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