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- PDB-6hdk: R49A variant of beta-phosphoglucomutase from Lactococcus lactis c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hdk | |||||||||
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Title | R49A variant of beta-phosphoglucomutase from Lactococcus lactis complexed with aluminium tetrafluoride and beta-G6P to 1.2 A. | |||||||||
![]() | Beta-phosphoglucomutase | |||||||||
![]() | ISOMERASE / phosphoglucomutase / metal fluoride / transition state analog | |||||||||
Function / homology | ![]() beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Robertson, A.J. / Bisson, C. / Waltho, J.P. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 83.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ![]() 6hdlC ![]() 6hdmC ![]() 2wf6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/BG6.gif)
![](data/chem/img/BG6.gif)
#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.) ![]() Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: ![]() ![]() |
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#6: Sugar | ChemComp-BG6 / |
-Non-polymers , 5 types, 216 molecules ![](data/chem/img/ALF.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ALF / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→54.29 Å / Num. obs: 60728 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Rrim(I) all: 0.107 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.24→1.26 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.019 / Num. unique obs: 2904 / CC1/2: 0.53 / Rpim(I) all: 0.48 / Rrim(I) all: 1.131 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WF6 Resolution: 1.24→52.17 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.668 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.039 / 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: 16.05 Å2
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Refinement step | Cycle: 1 / Resolution: 1.24→52.17 Å
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Refine LS restraints |
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