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Yorodumi- PDB-3uun: Crystal Structure of N-terminal first spectrin repeat of dystrophin -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uun | ||||||
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Title | Crystal Structure of N-terminal first spectrin repeat of dystrophin | ||||||
Components | Dystrophin | ||||||
Keywords | STRUCTURAL PROTEIN / triple helical / Cell structure and stability / Cytoskeletal | ||||||
Function / homology | Function and homology information regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / regulation of voltage-gated calcium channel activity / negative regulation of peptidyl-cysteine S-nitrosylation / positive regulation of sodium ion transmembrane transporter activity / dystrophin-associated glycoprotein complex ...regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / regulation of voltage-gated calcium channel activity / negative regulation of peptidyl-cysteine S-nitrosylation / positive regulation of sodium ion transmembrane transporter activity / dystrophin-associated glycoprotein complex / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / peptide biosynthetic process / cell-substrate junction / motile cilium assembly / dystroglycan binding / vinculin binding / muscle cell development / costamere / neuron projection terminus / Striated Muscle Contraction / filopodium membrane / muscle organ development / structural constituent of muscle / muscle cell cellular homeostasis / myosin binding / maintenance of blood-brain barrier / nitric-oxide synthase binding / negative regulation of peptidyl-serine phosphorylation / Non-integrin membrane-ECM interactions / neuron development / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / skeletal muscle tissue development / regulation of ryanodine-sensitive calcium-release channel activity / response to muscle stretch / positive regulation of neuron differentiation / regulation of heart rate / filopodium / protein localization / structural constituent of cytoskeleton / sarcolemma / positive regulation of neuron projection development / Z disc / actin binding / protein-containing complex assembly / postsynaptic membrane / cytoskeleton / membrane raft / synapse / cell surface / protein-containing complex / zinc ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Muthu, M. / Richardson, K.A. / Sutherland-smith, A.J. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: The crystal structures of dystrophin and utrophin spectrin repeats: implications for domain boundaries Authors: Muthu, M. / Richardson, K.A. / Sutherland-Smith, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uun.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uun.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uun_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 3uun_full_validation.pdf.gz | 436.3 KB | Display | |
Data in XML | 3uun_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 3uun_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/3uun ftp://data.pdbj.org/pub/pdb/validation_reports/uu/3uun | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 13642.204 Da / Num. of mol.: 2 / Fragment: Spectrin Repeat, UNP residues 338-456 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DMD / Plasmid: pPRoExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P11532 #2: 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: 2.03 Å3/Da / Density % sol: 39.52 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K |
-Data collection
Diffraction | Mean temperature: 120 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2010 / Details: OSMIC BLUE CONFOCAL MIRRORS | |||||||||||||||
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→33.24 Å / Num. all: 9999 / Num. obs: 9035 / % possible obs: 99.9 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 7.3 % / Biso Wilson estimate: 38.01 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 11.7 | |||||||||||||||
Reflection shell | Highest resolution: 2.3 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 11.7 / Num. unique all: 9999 / Rsym value: 0.605 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.582 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(I): 3.1 / ESU R Free: 0.06 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.399 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.51 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 663 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Highest resolution: 2.3 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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