+Open data
-Basic information
Entry | Database: PDB / ID: 1kze | ||||||
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Title | Complex of MBP-C and bivalent Man-terminated glycopeptide | ||||||
Components | MANNOSE-BINDING PROTEIN C | ||||||
Keywords | IMMUNE SYSTEM / SUGAR BINDING PROTEIN / protein-carbohydrate complex | ||||||
Function / homology | Function and homology information Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells ...Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / serine-type endopeptidase complex / phosphatidylinositol-4-phosphate binding / D-mannose binding / positive regulation of phagocytosis / antiviral innate immune response / complement activation, classical pathway / multivesicular body / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / innate immune response / signaling receptor binding / calcium ion binding / protein-containing complex / proteolysis / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Ng, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Orientation of bound ligands in mannose-binding proteins. Implications for multivalent ligand recognition. Authors: Ng, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kze.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kze.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kze_validation.pdf.gz | 451.6 KB | Display | wwPDB validaton report |
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Full document | 1kze_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 1kze_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1kze_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kze ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kze | HTTPS FTP |
-Related structure data
Related structure data | 1kwtC 1kwuC 1kwvC 1kwwC 1kwxC 1kwyC 1kwzC 1kx0C 1kx1C 1kzaC 1kzbC 1kzcC 1kzdC 1rdoS 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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1 |
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Unit cell |
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Details | non-physiological dimer |
-Components
#1: Protein | Mass: 12830.325 Da / Num. of mol.: 2 / Fragment: SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: MBL1 / Plasmid: pINOmpIIIA2 / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 / References: UniProt: P08661 #2: Sugar | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / | #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: 2.56 Å3/Da / Density % sol: 51.86 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-22 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 29, 1997 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 24443 / Num. obs: 24443 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2210 / Rsym value: 0.209 / % possible all: 88.9 |
Reflection | *PLUS Lowest resolution: 40 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 89.5 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.156 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1RDO Resolution: 1.8→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |