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Yorodumi- PDB-2ah5: Hydrolase, haloacid dehalogenase-like family protein SP0104 from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ah5 | ||||||
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Title | Hydrolase, haloacid dehalogenase-like family protein SP0104 from Streptococcus pneumoniae | ||||||
Components | COG0546: Predicted phosphatases | ||||||
Keywords | structural genomics / unknown function / MCSG / Streptococcus pneumoniae / hydrolase / haloacid dehalogenase-like / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å | ||||||
Authors | Binkowski, T.A. / Zhou, M. / Abdullah, J. / Collart, F. / Joachimiak, A. / MCSG / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Hydrolase, haloacid dehalogenase-like family protein SP0104 from Streptococcus pneumoniae Authors: Binkowski, T.A. / Zhou, M. / Abdullah, J. / Collart, F. / Joachimiak, A. / MCSG | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ah5.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ah5.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ah5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/2ah5 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/2ah5 | 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
#1: Protein | Mass: 23601.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP0104 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97T51, UniProt: A0A0H2UN22*PLUS |
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#2: 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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20 mM HEPES, 200mM NaCL and 1mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792348 Å |
Detector | Type: SBC-1 / Detector: CCD / Date: Apr 26, 2005 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792348 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→65.09 Å / Num. all: 20861 / Num. obs: 20861 / % possible obs: 90.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.74→1.8 Å / % possible all: 68.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.74→65.09 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.43 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.138 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.092 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→65.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.789 Å / Total num. of bins used: 20
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