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Yorodumi- PDB-7lnx: I146A mutant of the isopentenyl phosphate kinase from Candidatus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lnx | ||||||
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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 / isoprenoid biosynthetic process / kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Candidatus Methanomethylophilus alvus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 7lnx.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lnx.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lnx ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lnx | 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30491.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: I146A Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea) Gene: BKD89_07040 / Production host: Escherichia coli (E. coli) References: UniProt: A0A3G3II74, isopentenyl phosphate kinase |
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-Non-polymers , 5 types, 59 molecules
#2: Chemical | #3: Chemical | ChemComp-Y7D / ( | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-WOG / ( | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.04 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.1 M Bis-Tris pH 5.5 28% 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.42 Å / Num. obs: 22800 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 35.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.13 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2038 / CC1/2: 0.71 / Rpim(I) all: 0.531 / Rrim(I) all: 0.877 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: natvie structure Resolution: 2.3→39.42 Å / SU ML: 0.3594 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7721 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: 44.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.42 Å
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Refine LS restraints |
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LS refinement shell |
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