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Yorodumi- PDB-3kbb: Crystal structure of putative beta-phosphoglucomutase from Thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kbb | |||||||||
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Title | Crystal structure of putative beta-phosphoglucomutase from Thermotoga maritima | |||||||||
Components | Phosphorylated carbohydrates phosphatase TM_1254 | |||||||||
Keywords | HYDROLASE / arbohydrate metabolism / thermotoga maritima / cobalt / magnesium / manganese / metal-binding / nickel / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / carbohydrate metabolic process / hydrolase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermotoga maritima msb8 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å | |||||||||
Authors | Strange, R.W. / Antonyuk, S.V. / Ellis, M.J. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / Hasnain, S.S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of a putative beta-phosphoglucomutase (TM1254) from Thermotoga maritima. Authors: Strange, R.W. / Antonyuk, S.V. / Ellis, M.J. / Bessho, Y. / Kuramitsu, S. / Shinkai, A. / Yokoyama, S. / Hasnain, S.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kbb.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbb.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 3kbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbb ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbb | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24946.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima msb8 (bacteria) / Strain: MSB8 / Gene: bpgm, tm_1254 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(de3) References: UniProt: Q9X0Y1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: 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: 2.7 Å3/Da / Density % sol: 54.4 % / Mosaicity: 0.65 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.8M AMMONIUM SULFATE, 0.1M NA3 CITRATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 28, 2007 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7.1 % / Number: 195892 / Rmerge(I) obs: 0.046 / Χ2: 0.99 / D res high: 1.74 Å / D res low: 50 Å / Num. obs: 27547 / % possible obs: 94.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.74→31.61 Å / Num. all: 29058 / Num. obs: 27547 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 38 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.74→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1984 / % possible all: 70.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.74→31.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.405 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.29 Å2 / Biso mean: 28.09 Å2 / Biso min: 7.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→31.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.79 Å / Total num. of bins used: 20
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