+Open data
-Basic information
Entry | Database: PDB / ID: 2zyg | ||||||
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Title | Apo-form of dimeric 6-phosphogluconate dehydrogenase | ||||||
Components | 6-phosphogluconate dehydrogenase, decarboxylating | ||||||
Keywords | OXIDOREDUCTASE / NADP / pentose phosphate pathway / 6-phosphogluconate dehydrogenase / 6-phosphogluconate | ||||||
Function / homology | Function and homology information D-gluconate metabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt / NADP binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chen, Y.-Y. / Ko, T.-P. / Lo, L.-P. / Lin, C.-H. / Wang, A.H.-J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism Authors: Chen, Y.-Y. / Ko, T.-P. / Chen, W.-H. / Lo, L.-P. / Lin, C.-H. / Wang, A.H.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zyg.cif.gz | 211 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zyg.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/2zyg ftp://data.pdbj.org/pub/pdb/validation_reports/zy/2zyg | HTTPS FTP |
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-Related structure data
Related structure data | 2zyaC 2zydSC 3fwnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 53081.699 Da / Num. of mol.: 2 / Mutation: A134T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: NTUH-K2044 / Gene: gnd / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q762L5, UniProt: A0A0J9WZ66*PLUS, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) #2: 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: 2.06 Å3/Da / Density % sol: 40.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.12M diammonium hydrogen citrate, 20% PEG3350, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 12, 2006 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 51413 / Num. obs: 51259 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5044 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2zyd Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.0419
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