+Open data
-Basic information
Entry | Database: PDB / ID: 2fne | ||||||
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Title | The crystal structure of the 13th PDZ domain of MPDZ | ||||||
Components | Multiple PDZ domain protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Protein / SGC / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information tight junction assembly / apicolateral plasma membrane / bicellular tight junction / apical part of cell / postsynaptic density / apical plasma membrane / dendrite / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Papagrigoriou, E. / Berridge, G. / Johansson, C. / Colebrook, S. / Salah, E. / Burgess, N. / Smee, C. / Savitsky, P. / Bray, J. / Schoch, G. ...Papagrigoriou, E. / Berridge, G. / Johansson, C. / Colebrook, S. / Salah, E. / Burgess, N. / Smee, C. / Savitsky, P. / Bray, J. / Schoch, G. / Phillips, C. / Gileadi, C. / Soundarajan, M. / Yang, X. / Elkins, J.M. / Gorrec, F. / Turnbull, A. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions. Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fne.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fne.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fne_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 2fne_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 2fne_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 2fne_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/2fne ftp://data.pdbj.org/pub/pdb/validation_reports/fn/2fne | HTTPS FTP |
-Related structure data
Related structure data | 2bygSC 2fcfC 2gzvC 2he2C 2he4C 2i1nC 2iwnC 2iwoC 2iwpC 2iwqC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 1956 - 2048 / Label seq-ID: 25 - 117
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Details | Each of the three monomers found in the asu represents a biological unit |
-Components
#1: Protein | Mass: 12529.081 Da / Num. of mol.: 3 / Fragment: MPDZ domain, residues 1955-2042 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MPDZ, MUPP1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)R3 / References: UniProt: Q5VZ62, UniProt: O75970*PLUS #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: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 8% PEG P3350, 0.1M acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→39.5 Å / Num. all: 26633 / Num. obs: 26605 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0508 |
Reflection shell | Resolution: 1.83→1.95 Å / Rmerge(I) obs: 0.4753 / Mean I/σ(I) obs: 2.15 / Num. unique all: 4556 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2byg Resolution: 1.83→39.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.208 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.142 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.104 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→39.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 636 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.83→1.87 Å / Total num. of bins used: 20
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