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Yorodumi- PDB-5jxw: 2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jxw | ||||||
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Title | 2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Neplanocin-A and NAD | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / S-adenosylhomocysteinase / Neplanocin-A / 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: 2.25 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: 2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Neplanocin-A 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jxw.cif.gz | 787.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jxw.ent.gz | 656 KB | Display | PDB format |
PDBx/mmJSON format | 5jxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jxw_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 5jxw_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5jxw_validation.xml.gz | 75.8 KB | Display | |
Data in CIF | 5jxw_validation.cif.gz | 105.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/5jxw ftp://data.pdbj.org/pub/pdb/validation_reports/jx/5jxw | HTTPS FTP |
-Related structure data
Related structure data | 5hm8S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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) / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q5CPH1, adenosylhomocysteinase |
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-Non-polymers , 6 types, 771 molecules
#2: Chemical | ChemComp-6OS / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3),1mM NeplanocinA; Screen: Classics II (D7), 0.1M Bis-Tris-HCL (pH 6.5), 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 96622 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 41.6 Å2 / CC1/2: 0.87 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB-5HM8 Resolution: 2.25→29.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 13.603 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.216 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.575 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→29.93 Å
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Refine LS restraints |
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