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Yorodumi- PDB-6h8w: Beta-phosphoglucomutase from Lactococcus lactis in an open confor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h8w | |||||||||
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Title | Beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with aluminium tetrafluoride to 1.9 A. | |||||||||
Components | Beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / phosphoglucomutase / aluminium tetrafluoride / metal fluoride / transition state analogue | |||||||||
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 / Resolution: 1.98 Å | |||||||||
Authors | Robertson, A.J. / Bisson, C. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Transition state of phospho-enzyme hydrolysis in beta-phosphoglucomutase. Authors: Robertson, A.J. / Bisson, C. / Waltho, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h8w.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h8w.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 6h8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/6h8w ftp://data.pdbj.org/pub/pdb/validation_reports/h8/6h8w | HTTPS FTP |
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-Related structure data
Related structure data | 6h8uC 6h8vC 6h8xC 6h8yC 6h8zC 6h90C 6h93C 6h94C 6hdfC 6hdgC 6hdhC 6hdiC 6hdjC 6hdkC 6hdlC 6hdmC 2wheS S: Starting model for refinement C: citing same article (ref.) |
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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: 24239.594 Da / Num. of mol.: 1 / Mutation: K125R, Y206H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ALF / |
#4: 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: 2.39 Å3/Da / Density % sol: 48.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Crystals initially grown as open beta-phosphoglucomutase crystals, using 24-32% PEG 4000, 200mM sodium acetate, 50 mM TRIS buffer pH 7.5. Crystals were cryoprotected in their original mother ...Details: Crystals initially grown as open beta-phosphoglucomutase crystals, using 24-32% PEG 4000, 200mM sodium acetate, 50 mM TRIS buffer pH 7.5. Crystals were cryoprotected in their original mother liquor with the addition of 25% ethylene glycol, 5 mM aluminium chloride and 20 mM sodium fluoride. PH range: 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→40.44 Å / Num. all: 71414 / Num. obs: 19779 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.075 / Rrim(I) all: 0.156 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.738 / Num. unique obs: 1193 / CC1/2: 0.576 / Rpim(I) all: 0.459 / Rrim(I) all: 0.969 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WHE Resolution: 1.98→40.44 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.948 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.376 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→40.44 Å
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Refine LS restraints |
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