[English] 日本語
Yorodumi- PDB-5jpi: 2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jpi | ||||||
---|---|---|---|---|---|---|---|
Title | 2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with D-Eritadenine and NAD | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / S-adenosylhomocysteinase / D-Eritadenine / NAD / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Cryptosporidium parvum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with D-Eritadenine and NAD. Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jpi.cif.gz | 815.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jpi.ent.gz | 676.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jpi_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jpi_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5jpi_validation.xml.gz | 81.7 KB | Display | |
Data in CIF | 5jpi_validation.cif.gz | 118 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/5jpi ftp://data.pdbj.org/pub/pdb/validation_reports/jp/5jpi | HTTPS FTP |
-Related structure data
Related structure data | 5hm8S S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 56200.676 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q5CPH1, adenosylhomocysteinase |
---|
-Non-polymers , 9 types, 1248 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-DEA / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PO4 / | #8: Chemical | #9: Chemical | ChemComp-TRS / | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.1 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 7.9 MG/ML, 0.5M SODIUM CHLORIDE, 0.1M TRIS HCL (PH 8.3), DEA; Screen: JCSG+ (A11), 0.2M Ammonium phosphate, 0.1M TRIS-HCL (pH 8.5), 50% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 136687 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 32.1 Å2 / CC1/2: 0.887 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HM8 Resolution: 2.15→29.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 8.386 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.237 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→29.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|