+Open data
-Basic information
Entry | Database: PDB / ID: 2yyo | ||||||
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Title | Crystal structure of human SPRY domain | ||||||
Components | SPRY domain-containing protein 3 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SPRY domain / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information small GTPase binding => GO:0031267 / cytoskeleton organization / cell surface receptor signaling pathway / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Kishishita, S. / Uchikubo-Kamo, T. / Murayama, K. / Terada, T. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Shirouzu, M. / Wang, B.C. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human SPRY domain Authors: Kishishita, S. / Uchikubo-Kamo, T. / Murayama, K. / Terada, T. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Shirouzu, M. / Wang, B.C. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yyo.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yyo.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yyo ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yyo | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18261.812 Da / Num. of mol.: 1 / Fragment: SPRY domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPRYD3 / Plasmid: PK050905-07 / Production host: Cell-free protein synthesis / References: UniProt: Q8NCJ5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.02 % / Description: The file contains Friedel pairs. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 1.6M Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9789, 0.9793, 0.971 | ||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2006 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si II / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 18943 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 24.5 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.098 / Net I/σ(I): 78.6 | ||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Mean I/σ(I) obs: 20.4 / Rsym value: 0.348 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→26.05 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 213101.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: The file contains Friedel pairs.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.1519 Å2 / ksol: 0.339151 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→26.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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