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Yorodumi- PDB-3d53: 2.2 A crystal structure of inorganic pyrophosphatase from Rickett... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d53 | ||||||
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Title | 2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii | ||||||
Components | Inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / RICKETTSIA / INORGANIC / PYROPHOSPHATASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Magnesium / Metal-binding | ||||||
Function / homology | Function and homology information inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rickettsia prowazekii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: 2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii. Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d53.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d53.ent.gz | 175.1 KB | Display | PDB format |
PDBx/mmJSON format | 3d53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/3d53 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/3d53 | HTTPS FTP |
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-Related structure data
Related structure data | 2eipS S: Starting model for refinement |
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Similar structure data | |
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: 19629.762 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia prowazekii (bacteria) / Strain: Madrid E / Gene: ppa, RP589 / Plasmid: pET28-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZCW5, inorganic diphosphatase #2: Chemical | ChemComp-CL / #3: Chemical | #4: 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: 2.36 Å3/Da / Density % sol: 47.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 2.5M NaCl, 0.1M Na acetate pH 4.5, 0.2M Li2SO4, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2008 / Details: Adjustable focusing mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→34.94 Å / Num. obs: 56518 / % possible obs: 98.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2EIP Resolution: 2.2→33.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.013 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.576 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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