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Yorodumi- PDB-6qzg: Beta-glucose 1,6-bisphosphonate bound to wild type beta-phosphogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qzg | |||||||||
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Title | Beta-glucose 1,6-bisphosphonate bound to wild type beta-phosphoglucomutse in an open conformation. | |||||||||
Components | Beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / synthetic phosphorane inhibitor / phosphoglucomutase | |||||||||
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: 2.47 Å | |||||||||
Authors | Robertson, A.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Beta-glucose 1,6-bisphosphonate bound to wild type beta-phosphoglucomutse in an open conformation. Authors: Robertson, A.J. / 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 | 6qzg.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qzg.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 6qzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qzg_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6qzg_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6qzg_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 6qzg_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/6qzg ftp://data.pdbj.org/pub/pdb/validation_reports/qz/6qzg | HTTPS FTP |
-Related structure data
Related structure data | 2wheS S: Starting model for refinement |
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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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria) Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase #2: Chemical | #3: Sugar | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 24-34% PEG 4000 50 mM TRIS ph 7.5 200 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 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: 2.47→58.67 Å / Num. obs: 16554 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.082 / Rrim(I) all: 0.162 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.47→2.53 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1221 / CC1/2: 0.47 / Rpim(I) all: 0.559 / Rrim(I) all: 1.12 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WHE Resolution: 2.47→58.66 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.867 / SU B: 12.567 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.785 / ESU R Free: 0.334 / 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: 41.377 Å2
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Refinement step | Cycle: LAST / Resolution: 2.47→58.66 Å
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Refine LS restraints |
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