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Yorodumi- PDB-3ipw: Crystal structure of hydrolase TatD family protein from Entamoeba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ipw | ||||||
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Title | Crystal structure of hydrolase TatD family protein from Entamoeba histolytica | ||||||
Components | Hydrolase TatD family protein | ||||||
Keywords | HYDROLASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / dysentery / liver abcess | ||||||
Function / homology | 3'-5' ssDNA/RNA exonuclease TatD-like / TatD related DNase / 3'-5'-DNA exonuclease activity / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Hydrolase TatD family protein Function and homology information | ||||||
Biological species | Entamoeba histolytica HM-1:IMSS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of hydrolase TatD family protein from Entamoeba histolytica Authors: Edwards, T.E. / Statnekov, J.B. / Staker, B.L. / 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 | 3ipw.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ipw.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ipw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/3ipw ftp://data.pdbj.org/pub/pdb/validation_reports/ip/3ipw | HTTPS FTP |
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-Related structure data
Related structure data | 3e2vS 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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Details | Monomer |
-Components
#1: Protein | Mass: 37512.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote) Gene: EHI_119490 / Production host: Escherichia coli (E. coli) / References: UniProt: C4M7X7 |
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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: 2.09 Å3/Da / Density % sol: 41.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: JCSG+ condition D1, 24% PEG 1500, 20% glycerol, 44.6 mg/mL protein, crystal tracking ID 202317d1, pH 7.5, 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: Aug 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 23615 / % possible obs: 98.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.073 / Χ2: 1.034 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.45 / Num. unique all: 2166 / Χ2: 0.971 / % possible all: 93.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 57.35 / 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: 3e2v clipped to contain only homologous sections Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.83 / SU B: 3.68 / SU ML: 0.107 / SU R Cruickshank DPI: 0.176 / SU Rfree: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 56.28 Å2 / Biso mean: 25.689 Å2 / Biso min: 10.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.951→2.001 Å / Total num. of bins used: 20
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