+Open data
-Basic information
Entry | Database: PDB / ID: 3ojd | ||||||
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Title | Anti-Indolicidin monoclonal antibody V2D2 (Fab fragment) | ||||||
Components | (Fab V2D2) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Beta-sandwich Immunoglobulin fold / Antigen binding / Secreted protein / anti-indolicidin Fab / surrogate receptor | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lomash, S. / Salunke, D.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: An antibody as surrogate receptor reveals determinants of activity of an innate immune peptide antibiotic Authors: Lomash, S. / Nagpal, S. / Salunke, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ojd.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ojd.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ojd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ojd_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 3ojd_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 3ojd_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 3ojd_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/3ojd ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3ojd | HTTPS FTP |
-Related structure data
Related structure data | 1ymhS S: Starting model for refinement |
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Similar 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: 23415.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Light chain / Source: (natural) Mus musculus (house mouse) / Cell: B-cells / Organ: Spleen / Strain: BALB/c |
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#2: Antibody | Mass: 24398.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Heavy chain / Source: (natural) Mus musculus (house mouse) / Cell: B-cells / Organ: Spleen / Strain: BALB/c |
#3: 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: 2.25 Å3/Da / Density % sol: 45.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 10% PEG 1000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 21, 2006 / Details: mirrors |
Radiation | Monochromator: Ni FILTER CMF12 38Cu-6 (Osmic Inc.) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 31660 / Num. obs: 28494 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5 / Redundancy: 5.5 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YMH Resolution: 2→41.5 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011
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