+Open data
-Basic information
Entry | Database: PDB / ID: 6x1x | ||||||
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Title | PDZ domain from choanoflagellate GIPC (mbGIPC) | ||||||
Components | mbGIPC protein | ||||||
Keywords | SIGNALING PROTEIN / PDZ / protein-protein interaction / peptide-binding domain / choanoflagellate / Monosiga brevicollis | ||||||
Function / homology | PDZ domain-containing protein GIPC1/2/3 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PDZ domain-containing protein Function and homology information | ||||||
Biological species | Monosiga brevicollis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.198 Å | ||||||
Authors | Gao, M. / Amacher, J.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. Authors: Gao, M. / Mackley, I.G.P. / Mesbahi-Vasey, S. / Bamonte, H.A. / Struyvenberg, S.A. / Landolt, L. / Pederson, N.J. / Williams, L.I. / Bahl, C.D. / Brooks 3rd, L. / Amacher, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x1x.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x1x.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 6x1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x1x_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 6x1x_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 6x1x_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6x1x_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/6x1x ftp://data.pdbj.org/pub/pdb/validation_reports/x1/6x1x | HTTPS FTP |
-Related structure data
Related structure data | 6x1nC 6x1pC 6x1rC 6x20C 6x22C 6x23C 5v6bS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10406.070 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 94-187) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Gene: 39217 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9VCZ3 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M ammonium tartrate dibasic, pH 7.0, 12% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2019 | |||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.198→41.386 Å / Num. obs: 28166 / % possible obs: 91.4 % / Redundancy: 5.34 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 1 / Rsym value: 0.914 / Net I/σ(I): 31.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5V6B Resolution: 1.198→41.386 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.35 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.64 Å2 / Biso mean: 12.373 Å2 / Biso min: 3.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.198→41.386 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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