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Yorodumi- PDB-3fm9: Analysis of the Structural Determinants Underlying Discrimination... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fm9 | ||||||
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Title | Analysis of the Structural Determinants Underlying Discrimination between Substrate and Solvent in beta-Phosphoglucomutase Catalysis | ||||||
Components | Beta-phosphoglucomutase | ||||||
Keywords | ISOMERASE / HAD superfamily / phosphoaspartate / induced fit / domain movement | ||||||
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 subsp. lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Finci, L. / Lahiri, S. / Peisach, E. / Allen, K.N. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis. Authors: Dai, J. / Finci, L. / Zhang, C. / Lahiri, S. / Zhang, G. / Peisach, E. / Allen, K.N. / Dunaway-Mariano, D. #1: Journal: Science / Year: 2003 Title: The pentacovalent phosphorous intermediate of a phosphoryl transfer reaction Authors: Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fm9.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fm9.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fm9 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fm9 | HTTPS FTP |
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-Related structure data
Related structure data | 1zolS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24235.605 Da / Num. of mol.: 1 / Mutation: T16P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Gene: L0001, LL0429, pgmB / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71447, beta-phosphoglucomutase |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.001M DTT, 0.01M MgCl2, 25% PEG 3350, 0.2M NaCl, 0.1M bisTris pH 6.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 12, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 7122 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.151 / Χ2: 1.547 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, molecular replacement Starting model: PDB ENTRY 1ZOL Resolution: 2.7→39.598 Å / FOM work R set: 0.783 / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.428 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.79 Å2 / Biso mean: 32.56 Å2 / Biso min: 8.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→39.598 Å
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Refine LS restraints |
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