+Open data
-Basic information
Entry | Database: PDB / ID: 1igv | |||||||||
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Title | BOVINE CALBINDIN D9K BINDING MN2+ | |||||||||
Components | VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN, INTESTINAL | |||||||||
Keywords | METAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN / EF-HAND / MANGANESE BINDING | |||||||||
Function / homology | Function and homology information vitamin D binding / calcium-dependent protein binding / collagen-containing extracellular matrix / calcium ion binding / extracellular space / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Andersson, E.M. | |||||||||
Citation | Journal: Protein Sci. / Year: 1997 Title: Structural basis for the negative allostery between Ca(2+)- and Mg(2+)-binding in the intracellular Ca(2+)-receptor calbindin D9k. Authors: Andersson, M. / Malmendal, A. / Linse, S. / Ivarsson, I. / Forsen, S. / Svensson, L.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1igv.cif.gz | 27 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1igv.ent.gz | 17.5 KB | Display | PDB format |
PDBx/mmJSON format | 1igv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1igv_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 1igv_full_validation.pdf.gz | 421.8 KB | Display | |
Data in XML | 1igv_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 1igv_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/1igv ftp://data.pdbj.org/pub/pdb/validation_reports/ig/1igv | HTTPS FTP |
-Related 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: 8510.556 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: synthetic gene / Plasmid: picb1 / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 / References: UniProt: P02633 |
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#2: Chemical | ChemComp-MN / |
#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: 2.16 Å3/Da / Density % sol: 43 % Description: MN-CALBINDIN D9K WERE USED AS A DERIVATIVE FOR MIR SOLUTION OF MG-CALBINDIN D9K | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 5.6 Details: 65 % ammonium sulphate, 600 mM MnCl2, pH 5.6, EVAPORATION, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
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 RU200 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.2 Å / Num. all: 6482 / Num. obs: 6166 / % possible obs: 0.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.86→2 Å / Redundancy: 1 % / % possible all: 79 |
Reflection | *PLUS % possible obs: 95 % / Num. measured all: 17782 |
Reflection shell | *PLUS % possible obs: 79 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MG-CALBINDIN D9K Resolution: 1.85→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1083113 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.4 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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