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Yorodumi- PDB-1ru2: CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E.COLI HPPK(V83G/DEL84-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ru2 | ||||||
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Title | CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E.COLI HPPK(V83G/DEL84-89) WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN AT 1.48 ANGSTROM RESOLUTION (ORTHORHOMBIC FORM) | ||||||
Components | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | ||||||
Keywords | TRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / 6-HYDROXYMETHYLPTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / ANTIMICROBIAL AGENT / DRUG DESIGN / DELETION MUTANT | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Blaszczyk, J. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Essential Roles of a Dynamic Loop in the Catalysis of 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase. Authors: Blaszczyk, J. / Li, Y. / Wu, Y. / Shi, G. / Ji, X. / Yan, H. #1: Journal: Structure / Year: 1999 Title: Crystal Structure of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, a Potential Target for the Development of Novel Antimicrobial Agents Authors: Xiao, B. / Shi, G. / Chen, X. / Yan, H. / Ji, X. #2: Journal: Structure / Year: 2000 Title: Catalytic Center Assembly of Hppk as Revealed by the Crystal Structure of a Ternary Complex at 1.25 A Resolution Authors: Blaszczyk, J. / Shi, G. / Yan, H. / Ji, X. #3: 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 | 1ru2.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ru2.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ru2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/1ru2 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/1ru2 | HTTPS FTP |
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-Related structure data
Related structure data | 1rtzC 1ru1C 1q0nS 1f9y 1hq9 S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17094.482 Da / Num. of mol.: 1 / Mutation: V83G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FOLK, B0142 / 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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-Non-polymers , 5 types, 135 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-APC / | #5: Chemical | ChemComp-HHR / | #6: Water | ChemComp-HOH / | |
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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: 1.73 Å3/Da / Density % sol: 28.72 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG4000, MAGNESIUM CHLORIDE, ACETATE, GLYCEROL, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.00928 / Wavelength: 1.00928 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2001 / Details: MIRROR |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00928 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30 Å / Num. all: 20535 / Num. obs: 20535 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.414 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.6166 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 6.31 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.884 / Num. unique all: 1993 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.48 Å / Num. measured all: 152250 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1Q0N Resolution: 1.48→30 Å / Num. parameters: 11342 / Num. restraintsaints: 14982 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: FULL MATRIX LEAST-SQUARES PROCEDURE, WITH BLOCK OF PARAMETERS SET FOR EACH CYCLE OF ANISOTROPIC REFINEMENT
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.553 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.257 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 2 / Occupancy sum hydrogen: 1106 / Occupancy sum non hydrogen: 1336.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→30 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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