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Yorodumi- PDB-8u0l: Crystal structure of isopentenyl phosphate kinase from Thermococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u0l | ||||||
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Title | Crystal structure of isopentenyl phosphate kinase from Thermococcus paralvinellae bound to (E)-But-2-en-1-yl monophosphate and ADP | ||||||
Components | Isopentenyl phosphate kinase | ||||||
Keywords | TRANSFERASE / Alternate Mevalonate pathway IPK Amino acid kinase isoprenoids | ||||||
Function / homology | Function and homology information isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / glutamate 5-kinase activity / proline biosynthetic process / isoprenoid biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermococcus paralvinellae (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Singh, S. / Thomas, L.M. / Johnson, B.P. / Brown, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2024 Title: Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity. Authors: Johnson, B.P. / Mandal, P.S. / Brown, S.M. / Thomas, L.M. / Singh, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u0l.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u0l.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 8u0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/8u0l ftp://data.pdbj.org/pub/pdb/validation_reports/u0/8u0l | HTTPS FTP |
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-Related structure data
Related structure data | 8u0kC 8u0mC 8u0nC 7lntS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31962.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus paralvinellae (archaea) / Gene: TES1_0236 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 / References: UniProt: W0I5G2 #2: Chemical | #3: Chemical | Mass: 152.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9O4P / Feature type: SUBJECT OF INVESTIGATION #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: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.13 M magnesium formate, 10% PEG3350 |
-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: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→38.76 Å / Num. obs: 15975 / % possible obs: 98.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.083 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Rmerge(I) obs: 1.006 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2060 / CC1/2: 0.527 / Rpim(I) all: 0.783 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7LNT Resolution: 2.8→38.76 Å / SU ML: 0.459 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6648 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: 68.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→38.76 Å
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Refine LS restraints |
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LS refinement shell |
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