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- PDB-3mco: Crystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyropho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mco | ||||||
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Title | Crystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyrophosphokinase dihydropteroate synthase bifunctional enzyme from Francisella tularensis | ||||||
![]() | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase | ||||||
![]() | TRANSFERASE / folate / TIM barrel / kinase / synthase / HPPK / DHPS / pterin | ||||||
Function / homology | ![]() 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / Dihydropteroate synthase-like / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pemble IV, C.W. / Mehta, P.K. / Mehra, S. / Li, Z. / Lee, R.E. / White, S.W. | ||||||
![]() | ![]() Title: Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.dihydropteroate synthase bifunctional enzyme from Francisella tularensis. Authors: Pemble, C.W. / Mehta, P.K. / Mehra, S. / Li, Z. / Nourse, A. / Lee, R.E. / 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 | ![]() | 175.5 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mcmC ![]() 3mcnC ![]() 1twwS ![]() 2qx0S C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 50587.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LVS / Gene: folP/K, FTL_1265 / Plasmid: pET28 / Production host: ![]() ![]() #2: Chemical | ChemComp-PH2 / #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: TRIS, Na Acetate, PEG 4000, Glyerol, pH 8.0, vapor diffusion, sitting 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: Dec 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.2 Å / Num. all: 42690 / Num. obs: 41121 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.3→2.378 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3659 / % possible all: 84.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 2QX0, 1TWW Resolution: 2.3→38.251 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.98 / σ(I): 0 / 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: 43.759 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.44 Å2 / Biso mean: 40.282 Å2 / Biso min: 14.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→38.251 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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