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Yorodumi- PDB-6an6: Crystal structure of Escherichia coli HPPK in complex with bisubs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6an6 | ||||||
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Title | Crystal structure of Escherichia coli HPPK in complex with bisubstrate analogue inhibitor HP-72 | ||||||
Components | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | ||||||
Keywords | TRANSFERASE/INHIBITOR / alpha beta / TRANSFERASE-INHIBITOR complex | ||||||
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 / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Shaw, G.X. / Shi, G. / Ji, X. | ||||||
Citation | Journal: to be published Title: Bisubstrate analogue inhibitors of HPPK: Transition state mimetics Authors: Shaw, G.X. / Shi, G. / Ji, X. #1: 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. #2: Journal: Bioorg. Med. Chem. / Year: 2012 Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New designnnnn with improved properties Authors: Shi, G. / Shaw, G. / Liang, Y.-H. / Subburamann, P. / Li, Y. / Wu, Y. / Yan, H. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6an6.cif.gz | 135.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6an6.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 6an6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6an6_validation.pdf.gz | 997.8 KB | Display | wwPDB validaton report |
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Full document | 6an6_full_validation.pdf.gz | 1006.7 KB | Display | |
Data in XML | 6an6_validation.xml.gz | 17 KB | Display | |
Data in CIF | 6an6_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/6an6 ftp://data.pdbj.org/pub/pdb/validation_reports/an/6an6 | HTTPS FTP |
-Related structure data
Related structure data | 1eqmS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17966.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: folK, b0142, JW0138 / Plasmid: pDN2163 / Production host: Escherichia coli / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase #2: Chemical | #3: 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: 2.04 Å3/Da / Density % sol: 39.57 % / Mosaicity: 2.474 ° |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, NaCl etc. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 18, 2013 / Details: mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 16573 / % possible obs: 84.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.181 / % possible all: 74.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EQM Resolution: 2.3→29.68 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 31.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.68 Å
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Refine LS restraints |
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LS refinement shell |
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