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Yorodumi- PDB-43c9: CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9... -
+Open data
-Basic information
Entry | Database: PDB / ID: 43c9 | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY | ||||||
Components |
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Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å | ||||||
Authors | Thayer, M.M. / Getzoff, E.D. / Roberts, V.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Structural basis for amide hydrolysis catalyzed by the 43C9 antibody. Authors: Thayer, M.M. / Olender, E.H. / Arvai, A.S. / Koike, C.K. / Canestrelli, I.L. / Stewart, J.D. / Benkovic, S.J. / Getzoff, E.D. / Roberts, V.A. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Catalytic antibody model and mutagenesis implicate arginine in transition-state stabilization. Authors: Roberts, V.A. / Stewart, J. / Benkovic, S.J. / Getzoff, E.D. #2: Journal: Biochemistry / Year: 1994 Title: Site-directed mutagenesis of a catalytic antibody: an arginine and a histidine residue play key roles. Authors: Stewart, J.D. / Roberts, V.A. / Thomas, N.R. / Getzoff, E.D. / Benkovic, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 43c9.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb43c9.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 43c9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/3c/43c9 ftp://data.pdbj.org/pub/pdb/validation_reports/3c/43c9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Antibody | Mass: 12434.939 Da / Num. of mol.: 4 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ERZ9 #2: Antibody | Mass: 12846.444 Da / Num. of mol.: 4 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P01820 #3: Water | ChemComp-HOH / | Sequence details | THE FV FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT, E. A. KABAT, T. T. WU, H. M. PERRY, K. S. ...THE FV FRAGMENT IS NUMBERED BY THE CONVENTION | |
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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: 3.59 Å3/Da / Density % sol: 65.8 % | ||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 80% NACL, 50 MM MOPS PH 6.5 | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 |
Radiation | Monochromator: SI111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 65372 / % possible obs: 89.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.8 Å2 / Rsym value: 0.081 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.37 / % possible all: 0.564 |
Reflection | *PLUS Num. measured all: 234292 / Rmerge(I) obs: 0.081 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.2→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 Details: WITH THE EXCEPTION OF THE LAST LINKER RESIDUE (RESIDUE 0 IN CHAINS B, D, F, AND H), THE FLEXIBLE LINKER BETWEEN THE LIGHT AND HEAVY CHAINS WAS NOT OBSERVED IN THE CRYSTAL STRUCTURE.
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Displacement parameters | Biso mean: 54.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / σ(F): 2 / % reflection Rfree: 3.24 % / Rfactor Rwork: 0.21 / Rfactor obs: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 54.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.396 / Rfactor Rwork: 0.354 |