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- PDB-6h93: Beta-phosphoglucomutase from Lactococcus lactis with inorganic ph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h93 | |||||||||
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Title | Beta-phosphoglucomutase from Lactococcus lactis with inorganic phosphate bound in an open conformer to 1.8 A. | |||||||||
![]() | Beta-phosphoglucomutase | |||||||||
![]() | ISOMERASE / phosphoglucomutase / phosphate. | |||||||||
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 | ![]() | 105.5 KB | Display | ![]() |
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PDB format | ![]() | 79.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.3 KB | Display | ![]() |
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Full document | ![]() | 467.1 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h8uC ![]() 6h8vC ![]() 6h8wC ![]() 6h8xC ![]() 6h8yC ![]() 6h8zC ![]() 6h90C ![]() 6h94C ![]() 6hdfC ![]() 6hdgC ![]() 6hdhC ![]() 6hdiC ![]() 6hdjC ![]() 6hdkC ![]() 6hdlC ![]() 6hdmC ![]() 2wheS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24239.594 Da / Num. of mol.: 2 / Mutation: K125R, Y206H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 293 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PDO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 24-34% PEG 4000, 200 mM sodium acetate, 50 mM TRIS pH 7.5 PH range: 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→32.05 Å / Num. obs: 45050 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.426 / Num. unique obs: 2241 / CC1/2: 0.467 / Rpim(I) all: 0.583 / Rrim(I) all: 1.543 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WHE Resolution: 1.77→32.05 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.045 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.124 / 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: 30.83 Å2
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Refinement step | Cycle: 1 / Resolution: 1.77→32.05 Å
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Refine LS restraints |
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