+Open data
-Basic information
Entry | Database: PDB / ID: 5h0p | ||||||
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Title | Crystal structure of EF-hand protein mutant | ||||||
Components | EF-hand domain-containing protein D2 | ||||||
Keywords | METAL BINDING PROTEIN / EF-hand / Phosphorylation | ||||||
Function / homology | Function and homology information RHOD GTPase cycle / cadherin binding / membrane raft / calcium ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.862 Å | ||||||
Authors | Park, K.R. / An, J.Y. / Kang, J.Y. / Lee, J.G. / Youn, H.S. / Lee, Y. / Mun, S.A. / Jun, C.D. / Song, W.K. / Eom, S.H. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structural mechanism underlying regulation of human EFhd2/Swiprosin-1 actin-bundling activity by Ser183 phosphorylation. Authors: Park, K.R. / An, J.Y. / Kang, J.Y. / Lee, J.G. / Lee, Y. / Mun, S.A. / Jun, C.D. / Song, W.K. / Eom, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h0p.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h0p.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 5h0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h0p_validation.pdf.gz | 416.1 KB | Display | wwPDB validaton report |
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Full document | 5h0p_full_validation.pdf.gz | 416 KB | Display | |
Data in XML | 5h0p_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 5h0p_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/5h0p ftp://data.pdbj.org/pub/pdb/validation_reports/h0/5h0p | HTTPS FTP |
-Related structure data
Related structure data | 5i2lS 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: 13751.778 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-184 / Mutation: S183E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EFHD2, SWS1 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96C19 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.71 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M trimethlyamine-N-oxide dihydrate, 0.1 M Tris-HCl (pH 8.5), 20% (w/v) PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9897 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9897 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 8596 / % possible obs: 96.9 % / Redundancy: 13.2 % / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 6.6 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I2L Resolution: 1.862→29.796 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 27.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.862→29.796 Å
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Refine LS restraints |
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LS refinement shell |
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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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