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Yorodumi- PDB-6hdm: R49A variant of beta-phosphoglucomutase from Lactococcus lactis c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hdm | |||||||||
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Title | R49A variant of beta-phosphoglucomutase from Lactococcus lactis complexed with magnesium trifluoride and beta-G6P to 1.3 A. | |||||||||
Components | Beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / phosphoglucomutase / metal fluoride / transition state analog | |||||||||
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: 1.3 Å | |||||||||
Authors | Robertson, A.J. / Bisson, C. / Waltho, J.P. | |||||||||
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 | 6hdm.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hdm.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/6hdm ftp://data.pdbj.org/pub/pdb/validation_reports/hd/6hdm | HTTPS FTP |
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-Related structure data
Related structure data | 6h8uC 6h8vC 6h8wC 6h8xC 6h8yC 6h8zC 6h90C 6h93C 6h94C 6hdfC 6hdgC 6hdhC 6hdiC 6hdjC 6hdkC 6hdlC 2wf5S 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 24153.479 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, R49A 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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#5: Sugar | ChemComp-BG6 / |
-Non-polymers , 6 types, 213 molecules
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-MGF / | ||
#4: Chemical | ChemComp-NA / | ||
#6: Chemical | ChemComp-PDO / | ||
#7: Chemical | #8: 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: 2.19 Å3/Da / Density % sol: 43.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 24-34% PEG 4000 200mM sodium acetate 50mM TRIS pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→54.34 Å / Num. obs: 53048 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.263 / Num. unique obs: 2526 / CC1/2: 0.944 / Rpim(I) all: 0.138 / Rrim(I) all: 0.299 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WF5 Resolution: 1.3→48.27 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.114 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.053 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→48.27 Å
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Refine LS restraints |
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