+Open data
-Basic information
Entry | Database: PDB / ID: 2xph | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human SENP1 with the bound cobalt | ||||||
Components | SENTRIN-SPECIFIC PROTEASE 1 | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEASE / THIOL PROTEASE | ||||||
Function / homology | Function and homology information SUMO-specific endopeptidase activity / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / RHOF GTPase cycle / protein sumoylation / regulation of mRNA stability / apoptotic signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear membrane ...SUMO-specific endopeptidase activity / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / RHOF GTPase cycle / protein sumoylation / regulation of mRNA stability / apoptotic signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear membrane / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rimsa, V. / Eadsforth, T. / Hay, R.T. / Hunter, W.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: The Role of Co2+ in the Crystallization of Human Senp1 and Comments on the Limitations of Automated Refinement Protocols Authors: Rimsa, V. / Eadsforth, T. / Hay, R.T. / Hunter, W.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xph.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xph.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 2xph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xph_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2xph_full_validation.pdf.gz | 476.7 KB | Display | |
Data in XML | 2xph_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 2xph_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/2xph ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xph | HTTPS FTP |
-Related structure data
Related structure data | 2xreC 2iycS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28081.359 Da / Num. of mol.: 2 / Fragment: CATALYTIC FRAGMENT, RESIDUES 415-644 Source method: isolated from a genetically manipulated source Details: COBALT(II) ION, GLYCEROL / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHISTEV30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) GOLD References: UniProt: Q9P0U3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CO / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.76 % / Description: NONE |
---|---|
Crystal grow | Details: CRYSTALS FORMED FROM 1 TO 1 OF RESERVOIR SOLUTION (1.8 M AMMONIUM SULFATE, 50 MM COCL2 AND 100 MM MES PH 6.5) AND PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL (PH 8.0), AND 50 MM NACL). |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 13, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45 Å / Num. obs: 23808 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 53.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IYC Resolution: 2.4→66.66 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.805 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 407-417 IN CHAIN A AND 407-418 IN CHAIN B ARE DISORDERED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.721 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→66.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|