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Yorodumi- PDB-3mcn: Crystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyropho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mcn | ||||||
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Title | Crystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyrophosphokinase dihydropteroate synthase bifunctional enzyme from Francisella tularensis | ||||||
Components | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase | ||||||
Keywords | 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 / 2,6-diamino-5-nitropyrimidin-4(3H)-one / : Function and homology information | ||||||
Biological species | Francisella tularensis subsp. holarctica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Pemble IV, C.W. / Mehta, P.K. / Mehra, S. / Li, Z. / Lee, R.E. / White, S.W. | ||||||
Citation | Journal: Plos One / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mcn.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mcn.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 3mcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mcn_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 3mcn_full_validation.pdf.gz | 486.1 KB | Display | |
Data in XML | 3mcn_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 3mcn_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/3mcn ftp://data.pdbj.org/pub/pdb/validation_reports/mc/3mcn | HTTPS FTP |
-Related structure data
Related structure data | 3mcmC 3mcoC 1twwS 2qx0S C: citing same article (ref.) 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: 50587.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. holarctica (bacteria) Strain: LVS / Gene: folP/K, FTL_1265 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2A2W3 #2: Chemical | #3: Chemical | #4: 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: 2.36 Å3/Da / Density % sol: 47.96 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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: 2.2→46.1 Å / Num. all: 46715 / Num. obs: 43569 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3555 / % possible all: 76.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2QX0, 1TWW Resolution: 2.2→46.087 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.97 / 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: 48.924 Å2 / ksol: 0.367 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.82 Å2 / Biso mean: 41.198 Å2 / Biso min: 16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→46.087 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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