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Yorodumi- PDB-1pbt: The crystal structure of TM1154, oxidoreductase, sol/devB family ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pbt | ||||||
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Title | The crystal structure of TM1154, oxidoreductase, sol/devB family from Thermotoga maritima | ||||||
Components | 6-phosphogluconolactonase | ||||||
Keywords | HYDROLASE / OXIDOREDUCTASE / Structural genomics / alpha-beta / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information 6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt, oxidative branch / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Kim, Y. / Joachimiak, A. / Edwards, A. / Skarina, T. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure analysis of TM1154, oxidoreductase from Thermotoga maritima Authors: Kim, Y. / Joachimiak, A. / Edwards, A. / Skarina, T. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pbt.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pbt.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/1pbt ftp://data.pdbj.org/pub/pdb/validation_reports/pb/1pbt | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28261.623 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0N8, 6-phosphogluconolactonase |
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-Non-polymers , 5 types, 335 molecules
#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-FMT / | #6: 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: 1.86 Å3/Da / Density % sol: 33.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG MME 5000, ammonium sulfate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932, 0.97952, 0.946 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Apr 20, 2003 / Details: mirror | ||||||||||||
Radiation | Monochromator: double crystal, Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. all: 22136 / Num. obs: 22136 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.7 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3 / Num. unique all: 1476 / % possible all: 64.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→24.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 263854.87 / Data cutoff high rms absF: 263854.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.58 Å2 / ksol: 0.352069 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→24.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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