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Yorodumi- PDB-7lnu: Ternary complex of the Isopentenyl Phosphate Kinase from Candidat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lnu | ||||||
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Title | Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl 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: 2.5 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 | 7lnu.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lnu.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 7lnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lnu ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lnu | 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: 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 |
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-Non-polymers , 5 types, 170 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-IPE / | #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: 2.14 Å3/Da / Density % sol: 42.48 % |
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Crystal grow | Temperature: 275 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 20, 2016 / Details: Osmic Veri Max Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 18714 / % possible obs: 91 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.42 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.047 / Rrim(I) all: 0.1 / Χ2: 1.024 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.93 / Num. unique obs: 815 / CC1/2: 0.65 / Rpim(I) all: 0.394 / Rrim(I) all: 0.681 / Χ2: 0.925 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: cma apo model Resolution: 2.5→45.39 Å / SU ML: 0.3092 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.5766 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: 32.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.39 Å
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Refine LS restraints |
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LS refinement shell |
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