+
Open data
-
Basic information
Entry | Database: PDB / ID: 1k95 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of des(1-52)grancalcin with bound calcium | ||||||
![]() | GRANCALCIN | ||||||
![]() | METAL BINDING PROTEIN / penta-EF-hand protein / calcium binding protein | ||||||
Function / homology | ![]() azurophil granule lumen / membrane fusion / protein heterodimerization activity / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jia, J. / Borregaard, N. / Lollike, K. / Cygler, M. | ||||||
![]() | ![]() Title: Structure of Ca(2+)-loaded human grancalcin. Authors: Jia, J. / Borregaard, N. / Lollike, K. / Cygler, M. #1: ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 47.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 33 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 415.1 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k94C ![]() 1f4qS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.74 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
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 |