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- PDB-5tls: 2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tls | ||||||
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Title | 2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with DZ2002 and NAD | ||||||
![]() | Adenosylhomocysteinase | ||||||
![]() | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with DZ2002 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 807.3 KB | Display | ![]() |
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PDB format | ![]() | 669.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 79.3 KB | Display | |
Data in CIF | ![]() | 112.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hm8S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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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.) ![]() Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 1064 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ZD2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZD2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ZD2 / ( #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-PO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM ZD2002, 1mM NAD; 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 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: 2.4→30 Å / Num. obs: 109137 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.892 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HM8 Resolution: 2.4→29.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 11.727 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.187 / 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: 49.872 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→29.95 Å
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Refine LS restraints |
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