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Yorodumi- PDB-3ono: Crystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ono | ||||||
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Title | Crystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from Vibrio parahaemolyticus | ||||||
Components | Ribose/Galactose Isomerase | ||||||
Keywords | ISOMERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / alpha-beta-alpha sandwich / cytosol | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Kim, Y. / Volkart, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from Vibrio parahaemolyticus Authors: Kim, Y. / Volkart, L. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ono.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ono.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 3ono.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3ono ftp://data.pdbj.org/pub/pdb/validation_reports/on/3ono | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23150.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA0080 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q87K18 |
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#2: Chemical | ChemComp-GOL / |
#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: 2.59 Å3/Da / Density % sol: 52.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M postassium formate, 20 % (v/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97896 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 1, 2007 / Details: morrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97896 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 25080 / Num. obs: 25080 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.1 % / Biso Wilson estimate: 21.74 Å2 / Rsym value: 0.091 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 23.9 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 2153 / Rsym value: 0.492 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→30.452 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.833 Å2 / ksol: 0.337 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30.452 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: 11.2483 Å / Origin y: 3.3129 Å / Origin z: 18.9137 Å
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Refinement TLS group | Selection details: chain A |