+Open data
-Basic information
Entry | Database: PDB / ID: 8ihe | ||||||
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Title | Rv1122(gnd2) in Mycobacterium tuberculosis | ||||||
Components | Probable 6-phosphogluconate dehydrogenase,decarboxylating Gnd2 | ||||||
Keywords | HYDROLASE / dehydrogenase / tetramer | ||||||
Function / homology | Function and homology information organic acid catabolic process / D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt / NADP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Chen, Y.J. / Su, D. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Rv1122(gnd2) in Mycobacterium tuberculosis Authors: Chen, Y.J. / Su, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ihe.cif.gz | 249 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ihe.ent.gz | 202.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ihe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/8ihe ftp://data.pdbj.org/pub/pdb/validation_reports/ih/8ihe | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36400.074 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: gnd2, Rv1122 / Production host: Escherichia coli (E. coli) / References: UniProt: O06574 |
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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: 2.42 Å3/Da / Density % sol: 49.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20% PEG5000 0.2M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 37669 / % possible obs: 99.1 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.75→2.8 Å / Rmerge(I) obs: 0.972 / Num. unique obs: 1839 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→26.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.865 / SU B: 19.483 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.865 Å2
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Refinement step | Cycle: 1 / Resolution: 2.74→26.83 Å
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Refine LS restraints |
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