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Yorodumi- PDB-3sgw: Crystal structure of ribose-5-phosphate isomerase B RpiB from Coc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sgw | ||||||
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Title | Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid | ||||||
Components | ribose 5-phosphate isomerase | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Valley Fever / Coccidioidomycosis immitis / pathogenic fungus / RpiB / dust-borne pathogen / iodoacetic acid / covalent inhibitor / ribulose-5-phosphate / ribose-5-phosphate / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds / isomerase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Coccidioides immitis (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2011 Title: Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis. Authors: Edwards, T.E. / Abramov, A.B. / Smith, E.R. / Baydo, R.O. / Leonard, J.T. / Leibly, D.J. / Thompkins, K.B. / Clifton, M.C. / Gardberg, A.S. / Staker, B.L. / Van Voorhis, W.C. / Myler, P.J. / Stewart, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sgw.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sgw.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 3sgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/3sgw ftp://data.pdbj.org/pub/pdb/validation_reports/sg/3sgw | HTTPS FTP |
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-Related structure data
Related structure data | 3qd5C 3sdwSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19709.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_07932 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) References: UniProt: P0CL19, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds | ||||
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#2: Chemical | ChemComp-MLA / | ||||
#3: Chemical | #4: Chemical | #5: 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: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: protein at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2. Reservoir: 25% PEG 1500 and 0.1 M MIB (malonic acid, imidazole, boric acid), with 25% ethylene glycol as cryo-protection ...Details: protein at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2. Reservoir: 25% PEG 1500 and 0.1 M MIB (malonic acid, imidazole, boric acid), with 25% ethylene glycol as cryo-protection reagent, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 10, 2011 / Details: VariMax | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. all: 17530 / Num. obs: 16561 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 20.011 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 34.74 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3SDW Resolution: 1.7→49.08 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1573 / WRfactor Rwork: 0.131 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9104 / SU B: 3.235 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0931 / SU Rfree: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.3 Å2 / Biso mean: 13.745 Å2 / Biso min: 3.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→49.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 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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