+Open data
-Basic information
Entry | Database: PDB / ID: 2pf5 | ||||||
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Title | Crystal Structure of the Human TSG-6 Link Module | ||||||
Components | Tumor necrosis factor-inducible protein TSG-6 | ||||||
Keywords | CELL ADHESION / LINK MODULE / HYALURONAN-BINDING DOMAIN / ALPHA/BETA DOMAIN | ||||||
Function / homology | Function and homology information fibronectin fibril organization / hyaluronan metabolic process / ovarian cumulus expansion / hyaluronic acid binding / carboxylesterase activity / negative regulation of neutrophil chemotaxis / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway ...fibronectin fibril organization / hyaluronan metabolic process / ovarian cumulus expansion / hyaluronic acid binding / carboxylesterase activity / negative regulation of neutrophil chemotaxis / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / positive regulation of receptor clustering / negative regulation of inflammatory response / tertiary granule lumen / cell-cell signaling / ficolin-1-rich granule lumen / cell adhesion / positive regulation of cell migration / inflammatory response / calcium ion binding / Neutrophil degranulation / signal transduction / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Higman, V.A. / Mahoney, D.J. / Noble, M.E.M. / Day, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Plasticity of the TSG-6 HA-binding loop and mobility in the TSG-6-HA complex revealed by NMR and X-ray crystallography Authors: Higman, V.A. / Blundell, C.D. / Mahoney, D.J. / Redfield, C. / Noble, M.E. / Day, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pf5.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pf5.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 2pf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pf5 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pf5 | HTTPS FTP |
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-Related structure data
Related structure data | 1uuhS 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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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 10946.578 Da / Num. of mol.: 5 / Fragment: LINK_MODULE, RESIDUES 36-133 IN PREPROTEIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: See Day et al. (1996) Protein Expression & Purification 8, 1-16. Gene: TNFAIP6, TSG6 / Plasmid: PRK172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98066 #2: Chemical | #3: Chemical | ChemComp-2PE / #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: 4.12 Å3/Da / Density % sol: 70.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: A 2.5 ul drop formed from equal amounts of protein solution (7 mg/ml solution in approximately 25mM TrisHCl and 75mM NaCl) and well solution was equilibrated against 1 ml well solution (2 M ...Details: A 2.5 ul drop formed from equal amounts of protein solution (7 mg/ml solution in approximately 25mM TrisHCl and 75mM NaCl) and well solution was equilibrated against 1 ml well solution (2 M Ammonium Sulphate, 2 % v/v PEG 400 and 0.1M Sodium Hepes (pH 7.5)), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→88.04 Å / Num. obs: 69439 / % possible obs: 99.14 % / Redundancy: 4.08 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.35 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.98 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.51 / % possible all: 98.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UUH - crystal structure of CD44 Resolution: 1.9→88.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.679 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / 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: 21.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→88.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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