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Yorodumi- PDB-5lve: STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lve | ||||||
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Title | STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN | ||||||
Components | BENCE-JONES PROTEIN LEN | ||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / BENCE-JONES PROTEIN | ||||||
Function / homology | Function and homology information CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / 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 / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schiffer, M. / Huang, D.-B. / Chang, C.-H. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Change in dimerization mode by removal of a single unsatisfied polar residue located at the interface. Authors: Pokkuluri, P.R. / Cai, X. / Johnson, G. / Stevens, F.J. / Schiffer, M. #1: Journal: Structure / Year: 1998 Title: A domain flip as a result of a single amino-acid substitution. Authors: Pokkuluri, P.R. / Huang, D.B. / Raffen, R. / Cai, X. / Johnson, G. / Stevens, P.W. / Stevens, F.J. / Schiffer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lve.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lve.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lve_validation.pdf.gz | 411.1 KB | Display | wwPDB validaton report |
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Full document | 5lve_full_validation.pdf.gz | 413 KB | Display | |
Data in XML | 5lve_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 5lve_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/5lve ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lve | HTTPS FTP |
-Related structure data
Related structure data | 1qacC 1lveS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 12592.961 Da / Num. of mol.: 1 / Fragment: G KAPPA CHAIN V-IV, VARIABLE DOMAIN, LIGHT CHAIN / Mutation: Q89A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P01625, UniProt: P06312*PLUS |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | A ZN+2 ION (RESIDUE 200) AND THREE WATERS (RESIDUES 214, 274 AND 353) ARE LOCATED ON SYMMETRY AXES ...A ZN+2 ION (RESIDUE 200) AND THREE WATERS (RESIDUES 214, 274 AND 353) ARE LOCATED ON SYMMETRY AXES AND THEIR OCCUPANCY IS SET TO 0.5 |
Sequence details | Q89A MUTANT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 2.0 M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 1MM ZINC ACETATE | |||||||||||||||||||||||||
Crystal grow | *PLUS 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 7471 / % possible obs: 97 % / Redundancy: 10 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 6.8 / % possible all: 88.3 |
Reflection shell | *PLUS % possible obs: 88.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LVE WITH GLN89 CHANGED TO ALA Resolution: 2→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 388280.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 Details: BULK SOLVENT MODEL USED THE LAST TWO RESIDUES (LYS-107 AND ARG-108) ARE NOT WELL DEFINED IN THE DENSITY MAPS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.8 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.04 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 18
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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