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Yorodumi- PDB-5hv3: Rifampin phosphotransferase G527Y mutant in complex with AMPPNP f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hv3 | ||||||
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Title | Rifampin phosphotransferase G527Y mutant in complex with AMPPNP from Listeria monocytogenes | ||||||
Components | Phosphoenolpyruvate synthasePyruvate, water dikinase | ||||||
Keywords | TRANSFERASE / Antibiotic resistance / Rifampin / Phosphotransferase | ||||||
Function / homology | PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.118 Å | ||||||
Authors | Zhang, P. / Qi, X. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis of rifampin inactivation by rifampin phosphotransferase Authors: Qi, X. / Lin, W. / Ma, M. / Wang, C. / He, Y. / He, N. / Gao, J. / Zhou, H. / Xiao, Y. / Wang, Y. / Zhang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hv3.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hv3.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 5hv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/5hv3 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hv3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 98503.312 Da / Num. of mol.: 1 / Fragment: UNP residues 1-867 / Mutation: G527Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: ATE46_07415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2YLC8 |
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#2: Chemical | ChemComp-ANP / |
#3: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 20%(w/v) PEG3350, 200 mM sodium formate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: May 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 18949 / % possible obs: 97.2 % / Redundancy: 6.4 % / Net I/σ(I): 13.3 |
-Processing
Software |
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Refinement | Resolution: 3.118→34.508 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37 / 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: 3.118→34.508 Å
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Refine LS restraints |
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LS refinement shell |
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