+Open data
-Basic information
Entry | Database: PDB / ID: 3zhl | ||||||
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Title | The crystal structure of single domain antibody 8-14 scaffold | ||||||
Components | MG8-14 SCAFFOLD ANTIBODY | ||||||
Keywords | IMMUNE SYSTEM / SINGLE DOMAIN ANTIBODY | ||||||
Function / homology | Function and homology information CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | ||||||
Authors | Song, H.-N. / Woo, E.-J. / Lim, H.-K. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Directed Evolution of Human Heavy Chain Variable Domain (Vh) Using in Vivo Protein Fitness Filter. Authors: Kim, D. / Song, H. / Nam, H.J. / Kim, S. / Park, Y. / Park, J. / Woo, E. / Lim, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zhl.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zhl.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zhl ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zhl | HTTPS FTP |
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-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: 13815.226 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01764*PLUS |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.7 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.1M BIS-TRIS;PH5.5, 3M SODIUM CHLORIDE, 5% ETHYL ACETATE |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.5418 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 11157 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 20.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 44.3 |
Reflection shell | Resolution: 1.96→1.99 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.4 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→28.103 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 27.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.615 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.47→28.103 Å
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Refine LS restraints |
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LS refinement shell |
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