+Open data
-Basic information
Entry | Database: PDB / ID: 1odb | ||||||
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Title | THE CRYSTAL STRUCTURE OF HUMAN S100A12 - COPPER COMPLEX | ||||||
Components | CALGRANULIN C | ||||||
Keywords | METAL BINDING PROTEIN / METAL-BINDING PROTEIN / CALCIUM-BINDING PROTEIN / S100 PROTEIN / EF-HAND / CALCIUM BINDING / HOST-PARASITE RESPONSE | ||||||
Function / homology | Function and homology information mast cell activation / RAGE receptor binding / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endothelial cell migration / defense response to fungus / xenobiotic metabolic process / neutrophil chemotaxis / positive regulation of MAP kinase activity ...mast cell activation / RAGE receptor binding / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endothelial cell migration / defense response to fungus / xenobiotic metabolic process / neutrophil chemotaxis / positive regulation of MAP kinase activity / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of inflammatory response / calcium-dependent protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of NF-kappaB transcription factor activity / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / cytoskeleton / defense response to bacterium / inflammatory response / copper ion binding / innate immune response / calcium ion binding / Neutrophil degranulation / extracellular space / zinc ion binding / extracellular region / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Moroz, O.V. / Antson, A.A. / Grist, S.J. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Lukanidin, E.M. / Bronstein, I.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of the Human S100A12-Copper Complex: Implications for Host-Parasite Defence Authors: Moroz, O.V. / Antson, A.A. / Grist, S.J. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Lukanidin, E.M. / Bronstein, I.B. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: The Three-Dimensional Structure of Human S100A12 Authors: Moroz, O.V. / Antson, A.A. / Murshudov, G.N. / Maitlanddodson, G.G. / Wilson, K.S. / Skibshoj, I. / Lukanidin, E. / Bronstein, I.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1odb.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1odb.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1odb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/1odb ftp://data.pdbj.org/pub/pdb/validation_reports/od/1odb | HTTPS FTP |
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-Related structure data
Related structure data | 1e8aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 10793.212 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: CA2+ AND CU2+ BOUND FORM / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: GRANULOCYTE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80511 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Compound details | INVOLVED IN HOST_PARASITE RESPONSE AGAINST ONCHOCERCA VOLVULUS AND BRUGIA MALAYI. EXISTS AS A ...INVOLVED IN HOST_PARASITE RESPONSE AGAINST ONCHOCERCA | Sequence details | RECLONING RESULTED IN ADDITIONAL | |
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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: 3 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5-7% PEG 5K MME, 250MM NACL, 5MM CACL2,1MM CUCL2,0.1M NA-CACODYLATE PH 6.5; HANGING-DROP VAPOUR DIFFUSION + SEEDING |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.373 |
Detector | Date: May 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.373 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→25 Å / Num. obs: 39556 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.19→2.27 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / % possible all: 97.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E8A Resolution: 2.19→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.359 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→25 Å
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Refine LS restraints |
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