+Open data
-Basic information
Entry | Database: PDB / ID: 4q2p | ||||||
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Title | NHERF3 PDZ2 in Complex with a Phage-Derived Peptide | ||||||
Components | Na(+)/H(+) exchange regulatory cofactor NHE-RF3 | ||||||
Keywords | PROTEIN BINDING / PDZ | ||||||
Function / homology | Function and homology information positive regulation of cation transmembrane transport / carnitine transport / positive regulation of ion transmembrane transporter activity / scavenger receptor binding / xenobiotic detoxification by transmembrane export across the plasma membrane / positive regulation of protein localization to membrane / microvillus membrane / brush border / positive regulation of protein targeting to membrane / protein-membrane adaptor activity ...positive regulation of cation transmembrane transport / carnitine transport / positive regulation of ion transmembrane transporter activity / scavenger receptor binding / xenobiotic detoxification by transmembrane export across the plasma membrane / positive regulation of protein localization to membrane / microvillus membrane / brush border / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / PDZ domain binding / brush border membrane / apical plasma membrane / signaling receptor binding / protein-containing complex binding / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Appleton, B.A. / Wiesmann, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: A structural portrait of the PDZ domain family. Authors: Ernst, A. / Appleton, B.A. / Ivarsson, Y. / Zhang, Y. / Gfeller, D. / Wiesmann, C. / Sidhu, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q2p.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q2p.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 4q2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q2p_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 4q2p_full_validation.pdf.gz | 474.8 KB | Display | |
Data in XML | 4q2p_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4q2p_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2p ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2p | HTTPS FTP |
-Related structure data
Related structure data | 4q2nC 4q2oC 4q2qC 1g9oS 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: 10699.305 Da / Num. of mol.: 3 / Fragment: unp residues 132-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDZK1, CAP70, NHERF3, PDZD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T2W1 #2: Chemical | ChemComp-TRS / | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Sequence details | PHAGE-DERIVED PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER | |
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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: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 4.6 Details: 30% PEG 4000, 0.1 M sodium acetate (pH 4.6), 0.1 M magnesium chloride, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 29, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→20 Å / Num. obs: 18068 / % possible obs: 94.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.043 / Χ2: 1.016 / Net I/σ(I): 37.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1g9o Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.303 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.19 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.02 Å2 / Biso mean: 55.336 Å2 / Biso min: 26.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.092 Å / Total num. of bins used: 25
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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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