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Yorodumi- PDB-2nuz: crystal structure of alpha spectrin SH3 domain measured at room t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nuz | ||||||
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Title | crystal structure of alpha spectrin SH3 domain measured at room temperature | ||||||
Components | Spectrin alpha chain, brain | ||||||
Keywords | STRUCTURAL PROTEIN / SH3 / beta barrel / antiparallel beta sheet / room temperature | ||||||
Function / homology | Function and homology information actin filament capping / costamere / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Agarwal, V. / Faelber, K. / Hologne, M. / Chevelkov, V. / Oschkinat, H. / Diehl, A. / Reif, B. | ||||||
Citation | Journal: To be Published Title: Comparison of MAS solid-state NMR and X-ray crystallographic data in the analysis of protein dynamics in the solid state Authors: Agarwal, V. / Faelber, K. / Hologne, M. / Chevelkov, V. / Oschkinat, H. / Diehl, A. / Reif, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nuz.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nuz.ent.gz | 14.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nuz ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nuz | HTTPS FTP |
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-Related structure data
Related structure data | 1u06S 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
#1: Protein | Mass: 7229.244 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07751 |
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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: 2.57 Å3/Da / Density % sol: 52.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 200mM ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8856 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 2005 / Details: mirrows |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→32.58 Å / Num. all: 6761 / Num. obs: 6380 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 29.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 4.96 / Rsym value: 0.438 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U06 Resolution: 1.85→32.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.072 / SU ML: 0.071 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.113 / ESU R Free: 0.098 / 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: 28.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→32.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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