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Yorodumi- PDB-1bjf: CRYSTAL STRUCTURE OF RECOMBINANT BOVINE NEUROCALCIN DELTA AT 2.4 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bjf | ||||||
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Title | CRYSTAL STRUCTURE OF RECOMBINANT BOVINE NEUROCALCIN DELTA AT 2.4 ANGSTROMS | ||||||
Components | NEUROCALCIN DELTA | ||||||
Keywords | CALCIUM-BINDING / MYRISTOYLATION / NEURONAL SPECIFIC GUANYLATE CYCLASE ACTIVATOR | ||||||
Function / homology | Function and homology information Activation of Ca-permeable Kainate Receptor / regulation of systemic arterial blood pressure / clathrin binding / tubulin binding / calcium-mediated signaling / actin binding / calcium ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.4 Å | ||||||
Authors | Vijay-Kumar, S. / Kumar, V.D. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of recombinant bovine neurocalcin. Authors: Vijay-Kumar, S. / Kumar, V.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bjf.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bjf.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bjf_validation.pdf.gz | 371.9 KB | Display | wwPDB validaton report |
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Full document | 1bjf_full_validation.pdf.gz | 379.5 KB | Display | |
Data in XML | 1bjf_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 1bjf_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/1bjf ftp://data.pdbj.org/pub/pdb/validation_reports/bj/1bjf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.473089, -0.846549, 0.244009), Vector: |
-Components
#1: Protein | Mass: 22274.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Strain: DH5-ALPHA / Cellular location: CYTOPLASM / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli) / References: UniProt: P61602 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.1 / Details: pH 6.1 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-25 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. obs: 12105 / % possible obs: 84.3 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 54.2 |
Reflection shell | *PLUS % possible obs: 54.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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