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Yorodumi- PDB-7lnw: I146A mutant of the isopentenyl phosphate kinase from Candidatus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lnw | ||||||
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Title | I146A mutant of the isopentenyl phosphate kinase from Candidatus methanomethylophilus alvus | ||||||
Components | Isopentenyl phosphate kinase | ||||||
Keywords | TRANSFERASE / Phosphotransferase ATP Biocatalysis Isoprenoids Enzyme Promiscuity | ||||||
Function / homology | Function and homology information isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / glutamate 5-kinase activity / proline biosynthetic process / isoprenoid biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Candidatus Methanomethylophilus alvus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Thomas, L.M. / Singh, S. / Johnson, B.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus . Authors: Johnson, B.P. / Kumar, V. / Scull, E.M. / Thomas, L.M. / Bourne, C.R. / Singh, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lnw.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lnw.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 7lnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lnw ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lnw | 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: 30491.146 Da / Num. of mol.: 2 / Mutation: I146A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea) Gene: BKD89_07040 / Production host: Escherichia coli (E. coli) References: UniProt: A0A3G3II74, isopentenyl phosphate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.96 Å3/Da / Density % sol: 37.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.1 M Bis-Tris pH 5.5 28% w/v PEG 3350, 0.1 M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 25, 2020 / Details: Omsmic Vari-Max |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→30 Å / Num. obs: 21038 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.23 Å2 / Rpim(I) all: 0.074 / Rrim(I) all: 0.155 / Net I/σ(I): 8.86 |
Reflection shell | Resolution: 2.29→2.34 Å / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1051 / CC1/2: 0.754 / Rpim(I) all: 0.317 / Rrim(I) all: 0.584 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Solved Native Resolution: 2.29→28.68 Å / SU ML: 0.2794 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5299 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→28.68 Å
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Refine LS restraints |
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LS refinement shell |
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