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Yorodumi- PDB-1wlz: Crystal structure of DJBP fragment which was obtained by limited ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wlz | ||||||
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Title | Crystal structure of DJBP fragment which was obtained by limited proteolysis | ||||||
Components | CAP-binding protein complex interacting protein 1 isoform a | ||||||
Keywords | UNKNOWN FUNCTION / EF-hand like | ||||||
Function / homology | Function and homology information cell projection / cytoskeleton / calcium ion binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, SIR / Resolution: 1.6 Å | ||||||
Authors | Honbou, K. / Suzuki, N. / Horiuchi, M. / Taira, T. / Niki, T. / Ariga, H. / Inagaki, F. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of DJBP Fragment which was obtained by Limited Proteolysis Authors: Honbou, K. / Suzuki, N. / Horiuchi, M. / Taira, T. / Niki, T. / Ariga, H. / Inagaki, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wlz.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wlz.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/1wlz ftp://data.pdbj.org/pub/pdb/validation_reports/wl/1wlz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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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-Components
#1: Protein | Mass: 12062.537 Da / Num. of mol.: 4 / Fragment: RESIDUES 229-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H5C4, UniProt: Q5THR3*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: 2.06 Å3/Da / Density % sol: 40.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% PEG MME 2000, 0.1M Na Acetate pH 4.6, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2002 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. all: 51566 / Num. obs: 51566 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.042 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, SIR / Resolution: 1.6→19.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 455686.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.872 Å2 / ksol: 0.377187 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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