[English] 日本語
Yorodumi- PDB-1lvh: The Structure of Phosphorylated beta-phosphoglucomutase from Lact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lvh | ||||||
---|---|---|---|---|---|---|---|
Title | The Structure of Phosphorylated beta-phosphoglucomutase from Lactoccocus lactis to 2.3 angstrom resolution | ||||||
Components | beta-phosphoglucomutase | ||||||
Keywords | ISOMERASE / HAD superfamily / phosphoaspartate / aspartylphosphate | ||||||
Function / homology | Function and homology information beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
Citation | Journal: Biochemistry / Year: 2002 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: Journal: Acta Crystallogr.,Sect.D / Year: 2002 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lvh.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lvh.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lvh ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lvh | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 24319.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: PGMB / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P71447, beta-phosphoglucomutase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9792369, 0.9790073, 0.96112713 | ||||||||||||
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 |
| ||||||||||||
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 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.3→42.89 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: maximum likelihood target using amplitudes and phase probability distributions
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→42.89 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.24 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|