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Yorodumi- PDB-2jik: Crystal structure of PDZ domain of Synaptojanin-2 binding protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jik | ||||||
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Title | Crystal structure of PDZ domain of Synaptojanin-2 binding protein | ||||||
Components | SYNAPTOJANIN-2 BINDING PROTEIN | ||||||
Keywords | MEMBRANE PROTEIN / TRANSMEMBRANE / OUTER MEMBRANE / MITOCHONDRIA DISTRIBUTION / PDZ / MEMBRANE / SCAFFOLD / MITOCHONDRION | ||||||
Function / homology | Function and homology information negative regulation of sprouting angiogenesis / regulation of Notch signaling pathway / embryo development / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of endothelial cell migration / receptor clustering / negative regulation of endothelial cell proliferation / Rho protein signal transduction / regulation of endocytosis ...negative regulation of sprouting angiogenesis / regulation of Notch signaling pathway / embryo development / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of endothelial cell migration / receptor clustering / negative regulation of endothelial cell proliferation / Rho protein signal transduction / regulation of endocytosis / protein targeting / negative regulation of angiogenesis / postsynaptic density membrane / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / chemical synaptic transmission / basolateral plasma membrane / mitochondrial outer membrane / neuron projection / mitochondrion Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Tickle, J. / Phillips, C. / Pike, A.C.W. / Cooper, C. / Salah, E. / Elkins, J. / Turnbull, A.P. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Tickle, J. / Phillips, C. / Pike, A.C.W. / Cooper, C. / Salah, E. / Elkins, J. / Turnbull, A.P. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Pdz Domain of Synaptojanin-2 Binding Protein Authors: Tickle, J. / Phillips, C. / Pike, A.C.W. / Cooper, C. / Salah, E. / Elkins, J. / Turnbull, A.P. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jik.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jik.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jik_validation.pdf.gz | 433 KB | Display | wwPDB validaton report |
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Full document | 2jik_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 2jik_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 2jik_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jik ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jik | HTTPS FTP |
-Related structure data
Related structure data | 2jinC 2fe5S C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99955, -0.03004, -0.00035), Vector: |
-Components
#1: Protein | Mass: 11034.173 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 6-100 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P57105 #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: 1.88 Å3/Da / Density % sol: 34.75 % |
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Crystal grow | pH: 4 Details: 20% PEG6K, 1M LITHIUM CHLORIDE, 0.1M CITRATE PH4.0, pH 4.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→38.35 Å / Num. obs: 35482 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.3 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FE5 Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.4 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / 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: 9.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→30 Å
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Refine LS restraints |
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