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Yorodumi- PDB-6h90: K145A variant of beta-phosphoglucomutase from Lactococcus lactis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h90 | |||||||||
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Title | K145A variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by beryllium trifluoride to 1.3 A. | |||||||||
Components | Beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / phosphoglucomutase / beryllium trifluoride / phospho-enzyme analog / metal fluoride | |||||||||
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: 1.31 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 | 6h90.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h90.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 6h90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h90_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6h90_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6h90_validation.xml.gz | 13 KB | Display | |
Data in CIF | 6h90_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h90 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h90 | HTTPS FTP |
-Related structure data
Related structure data | 6h8uC 6h8vC 6h8wC 6h8xC 6h8yC 6h8zC 6h93C 6h94C 6hdfC 6hdgC 6hdhC 6hdiC 6hdjC 6hdkC 6hdlC 6hdmC 2wheS 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 , 1 types, 1 molecules A
#1: Protein | Mass: 24181.492 Da / Num. of mol.: 1 / Mutation: K145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (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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-Non-polymers , 5 types, 296 molecules
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-NA / | ||
#4: Chemical | ChemComp-BEF / | ||
#5: Chemical | ChemComp-EDO / #6: 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: 2.36 Å3/Da / Density % sol: 47.85 % |
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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 100mM TRIS pH 7.5 PH range: 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Sep 24, 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: 1.31→40.75 Å / Num. obs: 55835 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.31→1.34 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4062 / CC1/2: 0.539 / Rpim(I) all: 0.517 / Rrim(I) all: 1.335 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WHE Resolution: 1.31→40.75 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.684 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / 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: 16.262 Å2
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Refinement step | Cycle: 1 / Resolution: 1.31→40.75 Å
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Refine LS restraints |
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