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- PDB-3v5o: Structural and Mechanistic Studies of Catalysis and Sulfa Drug Re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v5o | ||||||
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Title | Structural and Mechanistic Studies of Catalysis and Sulfa Drug Resistance in Dihydropteroate Synthase | ||||||
![]() | Dihydropteroate synthase | ||||||
![]() | TRANSFERASE / Tim Barrel / DHPP and pABA | ||||||
Function / homology | Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yun, M. / Wu, Y. / Li, Z. / Zhao, Y. / Waddell, M.B. / Ferreira, A.M. / Lee, R.E. / Bashford, D. / White, S.W. | ||||||
![]() | ![]() Title: Catalysis and sulfa drug resistance in dihydropteroate synthase. Authors: Yun, M.K. / Wu, Y. / Li, Z. / Zhao, Y. / Waddell, M.B. / Ferreira, A.M. / Lee, R.E. / Bashford, D. / White, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.2 KB | Display | ![]() |
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PDB format | ![]() | 176.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.4 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tyaC ![]() 3tybC ![]() 3tycC ![]() 3tydC ![]() 3tyeC ![]() 3tyuC ![]() 3tyzC ![]() 3tzfC ![]() 3tznC ![]() 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: 32882.746 Da / Num. of mol.: 2 / Mutation: D184N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Bis-Tris propane, Lithium Sulfate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2011 / Details: Si 111 |
Radiation | Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 23961 / Num. obs: 23961 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rsym value: 0.079 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 1307 / Rsym value: 0.195 / % possible all: 49.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TWS Resolution: 2.5→48.19 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 27.965 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.506 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.09 Å2 / Biso mean: 75.2803 Å2 / Biso min: 19.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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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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