+Open data
-Basic information
Entry | Database: PDB / ID: 2wce | ||||||
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Title | calcium-free (apo) S100A12 | ||||||
Components | PROTEIN S100-A12 | ||||||
Keywords | METAL BINDING PROTEIN / CALCIUM SIGNALLING / APO / EF-HAND / CALCIUM FREE / S100 PROTEIN / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / calcium-dependent protein binding / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Moroz, O.V. / Blagova, E.V. / Wilkinson, A.J. / Wilson, K.S. / Bronstein, I.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The Crystal Structures of Human S100A12 in Apo Form and in Complex with Zinc: New Insights Into S100A12 Oligomerisation. Authors: Moroz, O.V. / Blagova, E.V. / Wilkinson, A.J. / Wilson, K.S. / 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. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Skibshoj, I. / Lukanidin, E.M. / Bronstein, I.B. #2: 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. / Bronstein, I.B. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: The Structure of S100A12 in a Hexameric Form and its Proposed Role in Receptor Signalling. Authors: Moroz, O.V. / Antson, A.A. / Dodson, E.J. / Burrell, H.J. / Grist, S.J. / Lloyd, R.M. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / 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 | 2wce.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wce.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wce_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
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Full document | 2wce_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 2wce_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2wce_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/2wce ftp://data.pdbj.org/pub/pdb/validation_reports/wc/2wce | HTTPS FTP |
-Related structure data
Related structure data | 2wc8C 2wcbC 2wcfC 1k9pS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 10905.040 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-92 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80511 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | EXTRA FOUR RESIDUES AT N TERMINUS MGGS, L76M SUBSTITUTI | |
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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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 1.4M NA-CITRATE, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→55.6 Å / Num. obs: 21533 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.7 |
Reflection shell | Highest resolution: 1.77 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.07 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K9P Resolution: 1.77→55.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.794 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→55.56 Å
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