[English] 日本語
Yorodumi- PDB-3g4e: Crystal structure of human senescence marker protein-30(SMP30)(Ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g4e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human senescence marker protein-30(SMP30)(Calcium bound) | ||||||
Components | Regucalcin | ||||||
Keywords | HYDROLASE / six bladed beta-propeller / gluconolcatonase / organophosphate hydrolase / regucalcin / calcium bound / Alternative splicing / Calcium / Cytoplasm / Phosphoprotein | ||||||
Function / homology | Function and homology information negative regulation of DNA catabolic process / negative regulation of RNA biosynthetic process / negative regulation of flagellated sperm motility / negative regulation of bone development / gluconolactonase / gluconolactonase activity / positive regulation of proteolysis involved in protein catabolic process / positive regulation of triglyceride biosynthetic process / negative regulation of nitric oxide biosynthetic process / positive regulation of fatty acid biosynthetic process ...negative regulation of DNA catabolic process / negative regulation of RNA biosynthetic process / negative regulation of flagellated sperm motility / negative regulation of bone development / gluconolactonase / gluconolactonase activity / positive regulation of proteolysis involved in protein catabolic process / positive regulation of triglyceride biosynthetic process / negative regulation of nitric oxide biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / L-ascorbic acid biosynthetic process / negative regulation of DNA biosynthetic process / positive regulation of ATP-dependent activity / enzyme regulator activity / regulation of calcium-mediated signaling / negative regulation of protein phosphorylation / kidney development / liver regeneration / intracellular calcium ion homeostasis / negative regulation of epithelial cell proliferation / spermatogenesis / calcium ion binding / negative regulation of apoptotic process / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å | ||||||
Authors | Chakraborti, S. / Bahnson, B.J. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions . Authors: Chakraborti, S. / Bahnson, B.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3g4e.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3g4e.ent.gz | 208.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g4e_validation.pdf.gz | 448.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3g4e_full_validation.pdf.gz | 473.4 KB | Display | |
Data in XML | 3g4e_validation.xml.gz | 32 KB | Display | |
Data in CIF | 3g4e_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/3g4e ftp://data.pdbj.org/pub/pdb/validation_reports/g4/3g4e | HTTPS FTP |
-Related structure data
Related structure data | 3g4hC 2ghsS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33073.488 Da / Num. of mol.: 2 / Fragment: UNP residues 3-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RGN, SMP30 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus / References: UniProt: Q15493 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.63 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 38% PEG 6000, 0.1M Tris-Hcl, 5mM calcium chloride, 5mM DTT, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2008 |
Radiation | Monochromator: KOHZU HLD-4 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→84.819 Å / Num. obs: 14159 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.056 |
Reflection shell | Resolution: 1.41→1.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 0.8 / Num. measured all: 89400 / Num. unique all: 14159 / Rsym value: 0.808 / % possible all: 91.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GHS Resolution: 1.42→8 Å / Num. parameters: 46695 / Num. restraintsaints: 57483 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.09 Å2 / Biso mean: 25.472 Å2 / Biso min: 9.19 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→8 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|