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Yorodumi- PDB-3twz: Phosphorylated Bacillus cereus phosphopentomutase in space group ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3twz | ||||||
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Title | Phosphorylated Bacillus cereus phosphopentomutase in space group P212121 | ||||||
Components | Phosphopentomutase | ||||||
Keywords | ISOMERASE / alkaline phosphatase superfamily / phosphorylation | ||||||
Function / homology | Function and homology information phosphopentomutase / phosphopentomutase activity / cellular metabolic compound salvage / 5-phosphoribose 1-diphosphate biosynthetic process / deoxyribonucleotide catabolic process / manganese ion binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Panosian, T.P. / Nanneman, D.P. / Bachmann, B.O. / Iverson, T.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Molecular Differences between a Mutase and a Phosphatase: Investigations of the Activation Step in Bacillus cereus Phosphopentomutase. Authors: Iverson, T.M. / Panosian, T.D. / Birmingham, W.R. / Nannemann, D.P. / Bachmann, B.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3twz.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3twz.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 3twz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3twz_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 3twz_full_validation.pdf.gz | 424.6 KB | Display | |
Data in XML | 3twz_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 3twz_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/3twz ftp://data.pdbj.org/pub/pdb/validation_reports/tw/3twz | HTTPS FTP |
-Related structure data
Related structure data | 3tx0C 3un2C 3un3C 3un5C 3unyC 3uo0C 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
#1: Protein | Mass: 44591.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: deoB, BC_4087 / Production host: Escherichia coli (E. coli) / References: UniProt: Q818Z9, phosphopentomutase | ||
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#2: Chemical | #3: 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: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 125 mM manganese chloride, 1.8 M ammonium citrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2010 |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 47942 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.75→1.81 Å / % possible all: 63.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.439 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.525 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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