+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+21 | ||||||
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Title | PDZ2 of LNX2 at 277K,single conformer model | ||||||
Components | Ligand of Numb protein X 2 | ||||||
Keywords | PROTEIN BINDING / Room temperature | ||||||
Function / homology | Function and homology information neural precursor cell proliferation / PDZ domain binding / neuron differentiation / ubiquitin-protein transferase activity / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.011 Å | ||||||
Authors | Hekstra, D.R. / White, K.I. / Socolich, M.A. / Ranganathan, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2016 Title: Electric-field-stimulated protein mechanics. Authors: Hekstra, D.R. / White, K.I. / Socolich, M.A. / Henning, R.W. / Srajer, V. / Ranganathan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e21.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e21.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 5e21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e21_validation.pdf.gz | 409.1 KB | Display | wwPDB validaton report |
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Full document | 5e21_full_validation.pdf.gz | 409.1 KB | Display | |
Data in XML | 5e21_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 5e21_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e21 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e21 | HTTPS FTP |
-Related structure data
Related structure data | 5e11C 5e1yC 5e22C 2vwrS 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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Unit cell |
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-Components
#1: Protein | Mass: 10310.739 Da / Num. of mol.: 1 / Fragment: Second PDZ domain (UNP residues 336-424) / Mutation: F338L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LNX2, PDZRN1 / Plasmid: pNic28 / Details (production host): SGC clone LNX2A-c033 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N448 |
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#2: Water | ChemComp-HOH / |
Sequence details | Authors state that the C-terminal extension (residues 425-428) contains a putative ligand motif. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25-29% PEG-300, 57 mM citric acid, 43 mM (Na2HPO4 pH 10.1) |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.011→28.95 Å / Num. obs: 35251 / % possible obs: 77.59 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.0507 / Net I/σ(I): 12.84 |
Reflection shell | Resolution: 1.011→1.047 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 0.45 / % possible all: 3.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VWR Resolution: 1.011→28.95 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.011→28.95 Å
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Refine LS restraints |
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LS refinement shell |
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