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Yorodumi- PDB-5fbs: Crystal structure of rifampin phosphotransferase RPH-Lm from List... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fbs | ||||||
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Title | Crystal structure of rifampin phosphotransferase RPH-Lm from Listeria monocytogenes in complex with ADP and magnesium | ||||||
Components | Phosphoenolpyruvate synthase | ||||||
Keywords | TRANSFERASE / antibiotic resistance / rifamycins / rifampin / phosphotransferase / ATP grasp domain / phosphohistidine domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ADENOSINE-5'-DIPHOSPHATE Function and homology information | ||||||
Biological species | Listeria monocytogenes serotype 4b str. F2365 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Stogios, P.J. / Wawrzak, Z. / Skarina, T. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Rifampin phosphotransferase is an unusual antibiotic resistance kinase. Authors: Stogios, P.J. / Cox, G. / Spanogiannopoulos, P. / Pillon, M.C. / Waglechner, N. / Skarina, T. / Koteva, K. / Guarne, A. / Savchenko, A. / Wright, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fbs.cif.gz | 328.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fbs.ent.gz | 266.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fbs_validation.pdf.gz | 753.7 KB | Display | wwPDB validaton report |
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Full document | 5fbs_full_validation.pdf.gz | 771.5 KB | Display | |
Data in XML | 5fbs_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 5fbs_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fbs ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fbs | HTTPS FTP |
-Related structure data
Related structure data | 5fbtSC 5fbuC S: Starting model for refinement C: citing same article (ref.) |
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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: 96991.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serotype 4b str. F2365 (bacteria) Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
Sequence details | Sequence matches to NCBI WP_010958733 which is not available in UNP database yet. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5 mM ADP, 20% PEG3350, 0.2 M calcium chloride, 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50.54 Å / Num. obs: 34559 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.59→2.66 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FBT Resolution: 2.59→50.54 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→50.54 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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