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Open data
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Basic information
Entry | Database: PDB / ID: 6ydl | |||||||||||||||||||||
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Title | Substrate-free beta-phosphoglucomutase from Lactococcus lactis | |||||||||||||||||||||
![]() | Beta-phosphoglucomutase | |||||||||||||||||||||
![]() | ISOMERASE / cis-trans proline isomerization / allomorphy / phosphoryl transfer | |||||||||||||||||||||
Function / homology | ![]() beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Wood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / Waltho, J.P. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Allomorphy as a mechanism of post-translational control of enzyme activity. Authors: Wood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / 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 | ![]() | 61.2 KB | Display | ![]() |
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PDB format | ![]() | 43.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 946.4 KB | Display | ![]() |
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Full document | ![]() | 946.4 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ydjC ![]() 6ydkC ![]() 6ydmC ![]() 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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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.) ![]() Gene: pgmB, LL0429, L0001 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 9.76 Å3/Da / Density % sol: 87.4 % / Description: Rod shaped |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, sodium acetate (200 mM), tris (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), beta-phosphoglucomutase (0.6 mM) PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2016 | |||||||||||||||||||||||||||
Radiation | Monochromator: 0.92819 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.52→44.65 Å / Num. obs: 36815 / % possible obs: 99.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.233 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Net I/σ(I): 18.8 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WHE Resolution: 1.52→44.65 Å / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.078 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 70.39 Å2 / Biso mean: 27.046 Å2 / Biso min: 15.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→44.65 Å
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