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Yorodumi- PDB-7zhw: Leishmania donovani Glucose 6-Phosphate Dehydrogenase complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zhw | ||||||
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Title | Leishmania donovani Glucose 6-Phosphate Dehydrogenase complexed with NADP(H) and Glucose 6-Phosphate | ||||||
Components | Glucose-6-phosphate 1-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Trypanosoma / Leishmania donovani / Glucose 6-Phosphate Dehydrogenase / G6P / NADP(H) / pentose phosphate pathway | ||||||
Function / homology | Function and homology information glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt / glucose metabolic process / NADP binding Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Fritz-Wolf, K. / Berneburg, I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Crystal structure of Leishmania donovani glucose 6-phosphate dehydrogenase reveals a unique N-terminal domain. Authors: Berneburg, I. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zhw.cif.gz | 269.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zhw.ent.gz | 180.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/7zhw ftp://data.pdbj.org/pub/pdb/validation_reports/zh/7zhw | HTTPS FTP |
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-Related structure data
Related structure data | 7zhtC 7zhuC 7zhvC 7zhxC 7zhyC 7zhzC C: citing same article (ref.) |
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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 / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 63407.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: g6pdh / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A2CIL3, glucose-6-phosphate dehydrogenase (NADP+) #5: Sugar | ChemComp-BG6 / | |
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-Non-polymers , 4 types, 12 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.96 Å3/Da / Density % sol: 58.39 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 12 % PEG 3000 and 200 mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→49.3 Å / Num. obs: 22716 / % possible obs: 99.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 124.7 Å2 / CC1/2: 1 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.3→3.4 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11462 / CC1/2: 0.7 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292122100 Resolution: 3.3→49.3 Å / SU ML: 0.6118 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.4726 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 144.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→49.3 Å
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Refine LS restraints |
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LS refinement shell |
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