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Yorodumi- PDB-8ctm: Crystal structure of the nucleoside hydrolase from Leishmania don... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ctm | ||||||
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Title | Crystal structure of the nucleoside hydrolase from Leishmania donovani. | ||||||
Components | Inosine-uridine preferring nucleoside hydrolase | ||||||
Keywords | HYDROLASE / ALPHA/BETA FOLD / LEISHMANIA | ||||||
Function / homology | Function and homology information purine nucleosidase / uridine nucleosidase activity / organonitrogen compound metabolic process / purine nucleosidase activity / nucleobase-containing compound metabolic process Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Chen, Y. / Tolbert, W.D. / Pazgier, M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of the nucleoside hydrolase from Leishmania donovani. Authors: Chen, Y. / Tolbert, W.D. / Pazgier, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ctm.cif.gz | 473.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ctm.ent.gz | 387.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ctm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ctm_validation.pdf.gz | 492.3 KB | Display | wwPDB validaton report |
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Full document | 8ctm_full_validation.pdf.gz | 505.3 KB | Display | |
Data in XML | 8ctm_validation.xml.gz | 53 KB | Display | |
Data in CIF | 8ctm_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8ctm ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8ctm | HTTPS FTP |
-Related structure data
Related structure data | 1ezrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 34278.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) Gene: iunh, CGC20_39000, CGC21_5445, LdCL_180021000, LDHU3_18.2000 Production host: Escherichia coli (E. coli) / References: UniProt: Q8WQX2, purine nucleosidase |
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-Non-polymers , 6 types, 857 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEG 3350 0.1 M MES saturated hypoxanthine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Monochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. obs: 263968 / % possible obs: 94.1 % / Redundancy: 3.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.057 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.73→1.76 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6560 / CC1/2: 0.82 / Rpim(I) all: 0.264 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ezr Resolution: 1.73→25.87 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 20.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→25.87 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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