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Yorodumi- PDB-1ex8: CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ex8 | ||||||
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Title | CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE COMPLEXED WITH HP4A, THE TWO-SUBSTRATE-MIMICKING INHIBITOR | ||||||
Components | 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE | ||||||
Keywords | TRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / PTERIN / ATP / BISUBSTRATE-MIMICKING INHIBITOR / ANTIMICROBIAL AGENT / DRUG DESIGN / SUBSTRATE SPECIFICITY / ACTIVE-SITE ARCHITECTURE | ||||||
Function / homology | Function and homology information 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Blaszczyk, J. / Ji, X. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2001 Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies. Authors: Shi, G. / Blaszczyk, J. / Ji, X. / Yan, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ex8.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ex8.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ex8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/1ex8 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/1ex8 | HTTPS FTP |
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-Related structure data
Related structure data | 1eqo S: Starting model for refinement |
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Similar 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: 17966.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-A4P / |
#5: Water | ChemComp-HOH / |
-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: 39.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, magnesium chloride, Tris-HCl, glycerol, acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 8 Details: drop consists of equal amounts of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 1999 / Details: 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: 1.85→40 Å / Num. all: 14188 / Num. obs: 12732 / % possible obs: 89.5 % / Observed criterion σ(F): 0.025 / Observed criterion σ(I): 0.05 / Redundancy: 3.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.056 / Num. unique all: 1384 / % possible all: 77.6 |
Reflection shell | *PLUS % possible obs: 77.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EQO 1eqo Resolution: 1.85→40 Å / Num. parameters: 5668 / Num. restraintsaints: 5447 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: Least-squares refinement using the Konnert-Hendrickson conjugate-gradient algorithm
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1478 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→40 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.212 / Rfactor obs: 0.185 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |