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Yorodumi- PDB-4emn: Crystal structure of RpfB catalytic domain in complex with benzamidine -
+Open data
-Basic information
Entry | Database: PDB / ID: 4emn | ||||||
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Title | Crystal structure of RpfB catalytic domain in complex with benzamidine | ||||||
Components | Probable resuscitation-promoting factor rpfB | ||||||
Keywords | HYDROLASE / alpha beta | ||||||
Function / homology | Function and homology information dormancy exit of symbiont in host / positive regulation of growth rate / Hydrolases / quorum sensing / regulation of cell population proliferation / hydrolase activity / negative regulation of gene expression / positive regulation of gene expression / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å | ||||||
Authors | Ruggiero, A. / Marchant, J. / Squeglia, F. / Makarov, V. / De Simone, A. / Berisio, R. | ||||||
Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2013 Title: Molecular determinants of inactivation of the resuscitation promoting factor B from Mycobacterium tuberculosis. Authors: Ruggiero, A. / Marchant, J. / Squeglia, F. / Makarov, V. / De Simone, A. / Berisio, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4emn.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4emn.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 4emn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/4emn ftp://data.pdbj.org/pub/pdb/validation_reports/em/4emn | HTTPS FTP |
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-Related structure data
Related structure data | 3eo5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 8591.399 Da / Num. of mol.: 4 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1038, rpfB, Rv1009 / Production host: Escherichia coli (E. coli) / References: UniProt: O05594, UniProt: P9WG29*PLUS #2: Chemical | ChemComp-BEN / #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: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.5% peg8000, 1M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→30 Å / Num. obs: 85254 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 1.17→1.21 Å / Rmerge(I) obs: 0.021 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3eo5 Resolution: 1.17→15 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.1 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.17→1.21 Å
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