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- PDB-1vl1: Crystal structure of 6-phosphogluconolactonase (TM1154) from Ther... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vl1 | ||||||
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Title | Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution | ||||||
![]() | 6-phosphogluconolactonase | ||||||
![]() | HYDROLASE / TM1154 / 6-PHOSPHOGLUCONOLACTONASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics | ||||||
Function / homology | ![]() 6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt, oxidative branch / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.9 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pbtS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26821.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 35.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop Details: 0.2M (NH4)2HCitrate, 20% PEG-3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Apr 2, 2004 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000034 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 24729 / % possible obs: 79.46 % / Redundancy: 3.86 % / Biso Wilson estimate: 23.98 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.59 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 2.93 / Num. unique all: 798 / Rsym value: 0.325 / % possible all: 26.04 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PBT Resolution: 1.55→37.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.158 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NOMINAL RESOLUTION IS 1.70 A WITH 2581 OBSERVED REFLECTIONS BETWEEN 1.70 - 1.55 A (35 % COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.367 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→37.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.591 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.1756 Å / Origin y: 21.4416 Å / Origin z: 17.9626 Å
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Refinement TLS group | Selection: ALL |