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Yorodumi- PDB-2gsi: Crystal Structure of a Murine Fab in Complex with an 11 Residue P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gsi | ||||||
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Title | Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FAB / IGG / STAPHYLOCOCCAL NUCLEASE | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / nucleic acid binding / blood microparticle / extracellular exosome ...endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / nucleic acid binding / blood microparticle / extracellular exosome / extracellular region / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Armstrong, A.A. / Amzel, L.M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease Authors: Armstrong, A.A. / Amzel, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gsi.cif.gz | 333.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gsi.ent.gz | 271.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gsi_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 2gsi_full_validation.pdf.gz | 492.7 KB | Display | |
Data in XML | 2gsi_validation.xml.gz | 39 KB | Display | |
Data in CIF | 2gsi_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gsi ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gsi | HTTPS FTP |
-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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Details | Chain A, Chain B, Chain W form an intact Fab with liganded peptide / Chain C, Chain D, Chain X form an intact Fab with liganded peptide / Chain E, Chain F, Chain Y form an intact Fab with liganded peptide / Chain G, Chain H, Chain Z form an intact Fab with liganded peptide |
-Components
#1: Antibody | Mass: 23483.934 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c #2: Antibody | Mass: 23789.611 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c / References: UniProt: Q6PF95 #3: Protein/peptide | Mass: 1319.570 Da / Num. of mol.: 4 / Fragment: Residues: 123-133 / Source method: obtained synthetically / Details: Peptide synthesized using standard Fmoc chemistry References: UniProt: Q8NXI6, UniProt: P00644*PLUS, micrococcal nuclease #4: Chemical | ChemComp-NA / #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: 2.59 Å3/Da / Density % sol: 52.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18% PEG 2000, 16% isopropanol, 0.1 M sodium citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2004 / Details: Pt coated toroidal Si mirror |
Radiation | Monochromator: Double flat Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 42035 / Num. obs: 42035 / % possible obs: 84.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.489 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries: 1f11, 2aju, 1f58, 1cr9 Resolution: 2.81→48.74 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.833 / SU B: 41.797 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.415 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→48.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.806→2.879 Å / Total num. of bins used: 20
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