+Open data
-Basic information
Entry | Database: PDB / ID: 1k95 | ||||||
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Title | Crystal structure of des(1-52)grancalcin with bound calcium | ||||||
Components | GRANCALCIN | ||||||
Keywords | METAL BINDING PROTEIN / penta-EF-hand protein / calcium binding protein | ||||||
Function / homology | Function and homology information azurophil granule lumen / membrane fusion / protein heterodimerization activity / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jia, J. / Borregaard, N. / Lollike, K. / Cygler, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of Ca(2+)-loaded human grancalcin. Authors: Jia, J. / Borregaard, N. / Lollike, K. / Cygler, M. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of human grancalcin, a member of the Penta-EF-Hand Protein family Authors: Jia, J. / Han, Q. / Borregaard, N. / Lollike, K. / Cygler, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallizaiton and preliminary X-ray analysis of human grancalcin, a novel Ca2+-binding protein in leukocytes Authors: Han, Q. / Jia, J. / Li, Y. / Lollike, K. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k95.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k95.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1k95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k95 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k95 | HTTPS FTP |
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-Related structure data
Related structure data | 1k94C 1f4qS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18771.225 Da / Num. of mol.: 1 / Fragment: residues 53-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P28676 |
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#2: 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: 1.98 Å3/Da / Density % sol: 37.74 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: ammoniun sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 12769 / Num. obs: 12769 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.083 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.23 / Rsym value: 0.31 / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 163585 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F4Q Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 11.5 % / Rfactor obs: 0.211 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |