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- PDB-1lvh: The Structure of Phosphorylated beta-phosphoglucomutase from Lact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lvh | ||||||
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Title | The Structure of Phosphorylated beta-phosphoglucomutase from Lactoccocus lactis to 2.3 angstrom resolution | ||||||
![]() | beta-phosphoglucomutase | ||||||
![]() | ISOMERASE / HAD superfamily / phosphoaspartate / aspartylphosphate | ||||||
Function / homology | ![]() beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
![]() | ![]() Title: Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis. Authors: Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. #1: ![]() Title: Crystallization and preliminary X-ray diffraction studies of beta-phosphoglucomutase from Lactococcus lactus Authors: Lahiri, S.D. / Zhang, G. / Radstrom, P. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.6 KB | Display | ![]() |
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PDB format | ![]() | 80.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.6 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 24319.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PGMB / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 16% PEG 3350, 0.15M Ammonium Floride, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 Details: Lahiri, S.D., (2002) Acta Crystallogr., Sect.D, 58, 324. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2001 / Details: Bent cylindrical Si-mirror (Rh coating) | ||||||||||||
Radiation | Monochromator: Si(111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. all: 25469 / Num. obs: 25469 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 12.3 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1746 / Rsym value: 0.191 / % possible all: 60.8 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 23862 / % possible obs: 91 % / Num. measured all: 420727 | ||||||||||||
Reflection shell | *PLUS % possible obs: 60.8 % / Rmerge(I) obs: 0.17 |
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Processing
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Refinement | Method to determine structure: ![]() Details: maximum likelihood target using amplitudes and phase probability distributions
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Displacement parameters | Biso mean: 42.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→42.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.24 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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