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Yorodumi- PDB-2qb6: Saccharomyces cerevisiae cytosolic exopolyphosphatase, sulfate complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qb6 | ||||||
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Title | Saccharomyces cerevisiae cytosolic exopolyphosphatase, sulfate complex | ||||||
Components | Exopolyphosphatase | ||||||
Keywords | HYDROLASE / a/b/a structure / DHH family phosphatase | ||||||
Function / homology | Function and homology information polyphosphate catabolic process / exopolyphosphatase / exopolyphosphatase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | White, S.A. / Ugochukwu, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The crystal structure of the cytosolic exopolyphosphatase from Saccharomyces cerevisiae reveals the basis for substrate specificity. Authors: Ugochukwu, E. / Lovering, A.L. / Mather, O.C. / Young, T.W. / White, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qb6.cif.gz | 184.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qb6.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/2qb6 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/2qb6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The protein is a monomer |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45109.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: PPX1, YHR201C / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38698, exopolyphosphatase |
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-Non-polymers , 6 types, 798 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: 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: 2.18 Å3/Da / Density % sol: 43.62 % Description: THIS ENTRY HAS BEEN RELEASED WITHOUT DEPOSITOR'S CHECKING AND CORRECTIONS, ONLY WITH NECESSARY PDB STAFF INTERVENTION. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 7% PEG 4000, 150 mM (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.4 Å / Num. all: 64994 / Num. obs: 64994 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.053 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 5374 / Rsym value: 0.194 / % possible all: 51.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→41.4 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.191 / SU ML: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.13 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→41.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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