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Yorodumi- PDB-7zhv: Leishmania donovani Glucose 6-Phosphate Dehydrogenase complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zhv | ||||||
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Title | Leishmania donovani Glucose 6-Phosphate Dehydrogenase complexed with 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 | 7zhv.cif.gz | 262.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zhv.ent.gz | 174.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/7zhv ftp://data.pdbj.org/pub/pdb/validation_reports/zh/7zhv | HTTPS FTP |
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-Related structure data
Related structure data | 7zhtC 7zhuC 7zhwC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.705178802526, 0.560104524289, -0.434747948055), (0.560917998042, -0.815752048838, -0.141136792829), (-0.433697885561, -0.144331274116, -0.889423761416)Vector: 50. ...NCS oper: (Code: given Matrix: (0.705178802526, 0.560104524289, -0.434747948055), Vector: |
-Components
#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+) #2: Sugar | ChemComp-BG6 / | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | 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: 3.01 Å3/Da / Density % sol: 59.07 % |
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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: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→39.1 Å / Num. obs: 22384 / % possible obs: 96.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 128.55 Å2 / CC1/2: 1 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.3→3.4 Å / Num. unique obs: 2211 / CC1/2: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292122100 Resolution: 3.3→39.1 Å / SU ML: 0.749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.1011 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: 138.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→39.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 7.87214556656 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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