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- PDB-2erf: Crystal Structure of the Thrombospondin-1 N-terminal Domain at 1.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2erf | ||||||
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Title | Crystal Structure of the Thrombospondin-1 N-terminal Domain at 1.45A Resolution | ||||||
![]() | Thrombospondin-1![]() | ||||||
![]() | SUGAR BINDING PROTEIN / ![]() | ||||||
Function / homology | ![]() negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Wang, J. / Lawler, J. | ||||||
![]() | ![]() Title: The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin. Authors: Tan, K. / Duquette, M. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Wang, J.H. / Lawler, J. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: ...SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: RSPWNRIPESGGDNSVFDIFELTGAARKGSGRRLVKGPDPSSPAFRIEDA NLIPPVPDDKFQDLVDAVRTEKGFLLLASLRQMKKTRGTLLALERKDHSG QVFSVVSNGKAGTLDLSLTVQGKQHVVSVEEALLATGQWKSITLFVQEDR AQLYIDCEKMENAELDVPIQSVFTRDLASIARLRIAKGGVNDNFQGVLQN VRFVFGTTPEDILRNKGCSSSTSVLLTLDNNVVNGSSPAIRTNTGHHHHHH THE PURIFIED PROTEIN WAS TREATED WITH CHYMOTRYPSIN AND RE-PURIFIED BEFORE CRYSTALLIZATION. THE EXACT N-TERMINAL OR C-TERMINAL SEQUENCES ARE NOT KNOWN. THE SEQRES REPRESENTS THE RESIDUES IN THE COORDINATES. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.5 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1z78SC ![]() 1za4C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 22901.035 Da / Num. of mol.: 1 / Fragment: N-terminal Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.7 % |
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG1500 and 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2005 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→30 Å / Num. all: 34155 / Num. obs: 34155 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2422 / % possible all: 68.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1Z78 Resolution: 1.45→22.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.702 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.962 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→22.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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