+Open data
-Basic information
Entry | Database: PDB / ID: 3pvn | ||||||
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Title | Triclinic form of Human C-Reactive Protein in complex with Zinc | ||||||
Components | C-reactive protein | ||||||
Keywords | IMMUNE SYSTEM / pentraxin family | ||||||
Function / homology | Function and homology information regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / Classical antibody-mediated complement activation ...regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / positive regulation of superoxide anion generation / acute-phase response / defense response to Gram-positive bacterium / inflammatory response / innate immune response / calcium ion binding / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Guillon, C. / Mavoungou Bigouagou, U. / Jeannin, P. / Delneste, Y. / Gouet, P. | ||||||
Citation | Journal: Protein Pept.Lett. / Year: 2014 Title: A Staggered Decameric Assembly of Human C-Reactive Protein Stabilized by Zinc Ions Revealed by X-ray Crystallography. Authors: Guillon, C. / Bigouagou, U.M. / Folio, C. / Jeannin, P. / Delneste, Y. / Gouet, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pvn.cif.gz | 872.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pvn.ent.gz | 714.1 KB | Display | PDB format |
PDBx/mmJSON format | 3pvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pvn_validation.pdf.gz | 597.7 KB | Display | wwPDB validaton report |
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Full document | 3pvn_full_validation.pdf.gz | 702.6 KB | Display | |
Data in XML | 3pvn_validation.xml.gz | 187.6 KB | Display | |
Data in CIF | 3pvn_validation.cif.gz | 253.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/3pvn ftp://data.pdbj.org/pub/pdb/validation_reports/pv/3pvn | HTTPS FTP |
-Related structure data
Related structure data | 3pvoC 1lj7S 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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Unit cell |
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-Components
#1: Protein | Mass: 23068.039 Da / Num. of mol.: 20 / Fragment: UNP residues 19-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRP, PTX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02741 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: 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: 2.41 Å3/Da / Density % sol: 48.99 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8 Details: 12% PEG 4000, 0.1M Tris-Hcl, 0.2M MgCl2, 0.05M LiCl, pH 8.0, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2008 |
Radiation | Monochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→20 Å / Num. all: 275048 / Num. obs: 275047 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.94 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.062 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 1.85 % / Mean I/σ(I) obs: 2.96 / Num. unique all: 19869 / Rsym value: 0.321 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LJ7 Resolution: 1.98→19.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.076 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.175 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.649 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.982→2.032 Å / Total num. of bins used: 20
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