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Yorodumi- PDB-7lnt: Ternary complex of the Isopentenyl Phosphate Kinase from Candidat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lnt | ||||||
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Title | Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to benzyl monophosphate and ATP | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Thomas, L.M. / Singh, S. / Scull, E.M. / Bourne, C.R. | ||||||
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 | 7lnt.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lnt.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lnt ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lnt | 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: 30533.225 Da / Num. of mol.: 2 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: Chemical | #5: 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: 2.13 Å3/Da / Density % sol: 42.23 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / Details: 0.1 M Bis-Tris pH 5.5 15% PEG 10000 |
-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: Sep 22, 2016 / Details: Osmic Veri Max Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 22277 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.17 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.109 / Χ2: 1.037 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.35→2.39 Å / Mean I/σ(I) obs: 2.89 / Num. unique obs: 999 / CC1/2: 0.874 / Rpim(I) all: 0.221 / Rrim(I) all: 0.412 / Χ2: 0.712 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CMA apo model Resolution: 2.35→29.45 Å / SU ML: 0.2472 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.529 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: 33.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→29.45 Å
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Refine LS restraints |
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LS refinement shell |
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