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- PDB-1ohq: Crystal structure of HEL4, a soluble human VH antibody domain res... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ohq | ||||||
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Title | Crystal structure of HEL4, a soluble human VH antibody domain resistant to aggregation | ||||||
![]() | IMMUNOGLOBULIN | ||||||
![]() | IMMUNOGLOBULIN / ANTIBODY / IMMUNE SYSTEM / FV FRAGMENT / HEL4 | ||||||
Function / homology | ![]() CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / 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 / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / 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 / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jespers, L. / Schon, O. / James, L.C. / Veprintsev, D. / Winter, G. | ||||||
![]() | ![]() Title: Crystal Structure of Hel4, a Soluble, Refoldable Human V(H) Single Domain with a Germ-Line Scaffold Authors: Jespers, L. / Schon, O. / James, L.C. / Veprintsev, D. / Winter, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.3 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.6 KB | Display | ![]() |
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Full document | ![]() | 406.5 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fgvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 12859.264 Da / Num. of mol.: 2 / Fragment: FV FRAGMENT, RESIDUES 1-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Date: Sep 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→70 Å / Num. obs: 19067 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.143 |
Reflection shell | *PLUS % possible obs: 96 % / Redundancy: 6 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FGV Resolution: 2→70 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→70 Å
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Refinement | *PLUS Rfactor Rfree: 0.256 / Rfactor Rwork: 0.177 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.259 / Rfactor Rwork: 0.183 |