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Yorodumi- PDB-3nas: The crystal structure of beta-phosphoglucomutase from Bacillus su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nas | ||||||
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Title | The crystal structure of beta-phosphoglucomutase from Bacillus subtilis | ||||||
Components | beta-phosphoglucomutase | ||||||
Keywords | ISOMERASE / PSI / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information beta-phosphoglucomutase / beta-phosphoglucomutase activity / hydrolase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of beta-phosphoglucomutase from Bacillus subtilis Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nas.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nas.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 3nas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/3nas ftp://data.pdbj.org/pub/pdb/validation_reports/na/3nas | 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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Details | dimer |
-Components
#1: Protein | Mass: 26286.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU34550, yvdM / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) Strain (production host): BL21 (DE3)-codon+RIL (p) - stratagene References: UniProt: O06995, beta-phosphoglucomutase #2: 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: 2.29 Å3/Da / Density % sol: 46.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS pH 6.5, 3.0 M Sodium chloride., VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→92.07 Å / Num. obs: 18400 / % possible obs: 99.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 58.49 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2650 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→59.589 Å / SU ML: 0.44 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.49 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.502 Å2 / ksol: 0.312 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.9 Å2
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Refinement step | Cycle: LAST / Resolution: 3→59.589 Å
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Refine LS restraints |
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LS refinement shell |
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