+Open data
-Basic information
Entry | Database: PDB / ID: 8yku | ||||||
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Title | PaThiL in complex with AMP-PNP and TMP | ||||||
Components | Thiamine-monophosphate kinase | ||||||
Keywords | PROTEIN BINDING / Complex / kinase | ||||||
Function / homology | Function and homology information thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Lin, J.Q. / Chung, Z. / Lescar, J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: ThiL in complex with AMP-PNP Authors: Lin, J.Q. / Lescar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yku.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yku.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 8yku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yku_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8yku_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8yku_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 8yku_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/8yku ftp://data.pdbj.org/pub/pdb/validation_reports/yk/8yku | HTTPS FTP |
-Related structure data
Related structure data | 7du3C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35495.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: thiL, CAZ10_30480, DY930_26150, FDK04_05055, IPC116_27470, IPC1323_04495, IPC1509_03965, IPC582_16370, IPC620_29520, NCTC13621_06786 Production host: Escherichia coli (E. coli) / References: UniProt: A0A232BM78, thiamine-phosphate kinase |
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-Non-polymers , 8 types, 219 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-TPS / | #5: Chemical | ChemComp-ANP / | #6: Chemical | #7: Chemical | ChemComp-PEG / | #8: Chemical | #9: 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: 3.77 Å3/Da / Density % sol: 67.38 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2M calcium acetate hydrate, 0.1M sodium cacodylate pH 6.5, 40% (v/v) PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953721724543 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953721724543 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→51.35 Å / Num. obs: 29549 / % possible obs: 99.98 % / Redundancy: 33.2 % / CC1/2: 0.998 / CC star: 1 / Rpim(I) all: 0.04168 / Net I/σ(I): 17.37 |
Reflection shell | Resolution: 2.17→2.248 Å / Num. unique obs: 2895 / CC1/2: 0.917 / CC star: 0.978 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→51.35 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.1932 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: 26.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→51.35 Å
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Refine LS restraints |
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LS refinement shell |
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