+Open data
-Basic information
Entry | Database: PDB / ID: 2jel | |||||||||
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Title | JEL42 FAB/HPR COMPLEX | |||||||||
Components |
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Keywords | COMPLEX (ANTIBODY/ANTIGEN) / ANTIBODY-PROTEIN COMPLEX / HISTIDINE-CONTAINING PROTEIN / MOLECULAR RECOGNITION / COMPLEX (ANTIBODY-ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) complex | |||||||||
Function / homology | Function and homology information phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Prasad, L. / Waygood, E.B. / Lee, J.S. / Delbaere, L.T.J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The 2.5 A resolution structure of the jel42 Fab fragment/HPr complex Authors: Prasad, L. / Waygood, E.B. / Lee, J.S. / Delbaere, L.T.J. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Evaluation of Mutagenesis for Epitope Mapping. Structure of an Antibody-Protein Antigen Complex Authors: Prasad, L. / Sharma, S. / Vandonselaar, M. / Quail, J.W. / Lee, J.S. / Waygood, E.B. / Wilson, K.S. / Dauter, Z. / Delbaere, L.T. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Epitope Mapping by Mutagenesis Distinguishes between the Two Tertiary Structures of the Histidine-Containing Protein Hpr Authors: Sharma, S. / Georges, F. / Delbaere, L.T. / Lee, J.S. / Klevit, R.E. / Waygood, E.B. #3: Journal: J.Biol.Chem. / Year: 1989 Title: Crystallization of the Complex of a Monoclonal Fab Fragment with the Histidine-Containing Protein of the Phosphoenolpyruvate: Sugar Phosphotransferase System of Escherichia Coli Authors: Delbaere, L.T. / Vandonselaar, M. / Quail, J.W. / Waygood, E.B. / Lee, J.S. #4: Journal: J.Biol.Chem. / Year: 1988 Title: Structure Determination of a Monoclonal Fab Fragment Specific for Histidine-Containing Protein of the Phosphoenolpyruvate: Sugar Phosphotransferase System of Escherichia Coli Authors: Prasad, L. / Vandonselaar, M. / Lee, J.S. / Delbaere, L.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jel.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jel.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 2jel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jel_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 2jel_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 2jel_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 2jel_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/2jel ftp://data.pdbj.org/pub/pdb/validation_reports/je/2jel | 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: 23860.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C | ||||
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#2: Antibody | Mass: 23094.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C | ||||
#3: Protein | Mass: 9129.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA04 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | RESIDUES OF THE FAB FRAGMENT ARE NUMBERED ACCORDING TO KABAT. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.8 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: the molar ratio of Fab fragment to HPr was approximately 1:2 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Apr 1, 1992 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→35 Å / Num. obs: 22067 / % possible obs: 96.6 % / Observed criterion σ(I): 5 / Redundancy: 2.7 % / Rsym value: 0.046 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.19 / % possible all: 93 |
Reflection | *PLUS Num. measured all: 47817 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 93 % / Num. unique obs: 1043 / Num. measured obs: 2784 / Rmerge(I) obs: 0.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: GLOOP2 FAB Resolution: 2.5→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.34 |