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Yorodumi- PDB-1neg: Crystal Structure Analysis of N-and C-terminal labeled SH3-domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1neg | ||||||
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Title | Crystal Structure Analysis of N-and C-terminal labeled SH3-domain of alpha-Chicken Spectrin | ||||||
Components | Spectrin alpha chain, brain | ||||||
Keywords | STRUCTURAL PROTEIN / SH3-domain fold / five antiparallel beta sheets | ||||||
Function / homology | Function and homology information costamere / actin filament capping / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Mueller, U. / Buessow, K. / Diehl, A. / Niesen, F.H. / Nyarsik, L. / Heinemann, U. | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2003 Title: Rapid purification and crystal structure analysis of a small protein carrying two terminal affinity tags Authors: Mueller, U. / Buessow, K. / Diehl, A. / Bartl, F.J. / Niesen, F.H. / Nyarsik, L. / Heinemann, U. | ||||||
History |
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Remark 999 | SEQUENCE ACCORDING TO THE AUTHOR, THIS IS PART OF A STREP2 TAG. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1neg.cif.gz | 27.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1neg.ent.gz | 17.2 KB | Display | PDB format |
PDBx/mmJSON format | 1neg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/1neg ftp://data.pdbj.org/pub/pdb/validation_reports/ne/1neg | HTTPS FTP |
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-Related structure data
Related structure data | 1shgS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9643.871 Da / Num. of mol.: 1 / Fragment: SH3-domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pQStrep2 / Production host: Escherichia coli (E. coli) / Strain (production host): scs1 / References: UniProt: P07751 |
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#2: Chemical | ChemComp-AZI / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Dioxane, MES, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 7, 2000 / Details: mirrors |
Radiation | Monochromator: Supper mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.1 Å / Num. all: 4077 / Num. obs: 3858 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.27 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.109 / Net I/σ(I): 13.05 |
Reflection shell | Resolution: 2.3→2.33 Å / Mean I/σ(I) obs: 1.94 / Num. unique all: 130 / Rsym value: 0.461 / % possible all: 95.6 |
Reflection | *PLUS Lowest resolution: 31 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.109 |
Reflection shell | *PLUS % possible obs: 95.6 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 1.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SHG Resolution: 2.3→31.09 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9616 Å2 / ksol: 0.410835 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze | Luzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.31 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→31.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 31.1 Å / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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