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Open data
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Basic information
Entry | Database: PDB / ID: 4d8a | ||||||
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Title | Crystal structure of B. anthracis DHPS with compound 21 | ||||||
![]() | Dihydropteroate synthase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / TIM narrel / Synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hammoudeh, D. / Lee, R.E. / White, S.W. | ||||||
![]() | ![]() Title: Structure-Based Design of Novel Pyrimido[4,5-c]pyridazine Derivatives as Dihydropteroate Synthase Inhibitors with Increased Affinity. Authors: Zhao, Y. / Hammoudeh, D. / Yun, M.K. / Qi, J. / White, S.W. / Lee, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.4 KB | Display | ![]() |
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PDB format | ![]() | 173.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d8zC ![]() 4d9pC ![]() 4dafC ![]() 4daiC ![]() 4db7C ![]() 1twsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32883.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C3P9L8, UniProt: Q81VW8*PLUS, dihydropteroate synthase #2: Chemical | ChemComp-LYS / | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 291 K / Method: hanging drop / pH: 9 Details: Lithium sulfate, Bis-Tris propane, pH 9.0, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→50 Å / Num. obs: 37033 / % possible obs: 92.7 % / Redundancy: 12.5 % / Rsym value: 0.087 / Net I/σ(I): 7.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TWS Resolution: 2.183→35.88 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.33 / σ(F): 0.13 / Phase error: 37.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.331 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.183→35.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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