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Yorodumi- PDB-2veg: Dihydropteroate synthase from Streptococcus pneumoniae: complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2veg | ||||||
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Title | Dihydropteroate synthase from Streptococcus pneumoniae: complex with 6-hydroxymethyl-7,8-dihydropterin monophosphate | ||||||
Components | DIHYDROPTEROATE SYNTHASE | ||||||
Keywords | TRANSFERASE / FOLIC ACID / BIOSYNTHESIS / ANTIBIOTIC RESISTANCE / STREPTOCOCCUS PNEUMONIAE / DIHYDROPTEROATE / FOLATE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to antibiotic / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Derrick, J. / Levy, C. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: Dihydropteroate Synthase from Streptococcus Pneumoniae: Structure, Ligand Recognition and Mechanism of Sulfonamide Resistance. Authors: Levy, C. / Minnis, D. / Derrick, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2veg.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2veg.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 2veg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2veg_validation.pdf.gz | 519.6 KB | Display | wwPDB validaton report |
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Full document | 2veg_full_validation.pdf.gz | 528.3 KB | Display | |
Data in XML | 2veg_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 2veg_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2veg ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2veg | HTTPS FTP |
-Related structure data
Related structure data | 2vefSC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.956, -0.23, 0.182), Vector: |
-Components
#1: Protein | Mass: 34457.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P59655, dihydropteroate synthase #2: Chemical | ChemComp-PMM / | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Sequence details | DIPEPTIDE 'IE' REMOVED FROM THE SEQUENCE AT POSITION 65, AS THIS CORRESPONDS TO THE SULPHONAMIDE ...DIPEPTIDE 'IE' REMOVED FROM THE SEQUENCE AT POSITION 65, AS THIS CORRESPOND | |
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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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NONE |
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Crystal grow | Details: 0.2 M AMMONIUM IODIDE AND 20% (W/V) POLYETHYLENE GLYCOL 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: OSMICMIRRORS |
Radiation | Monochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→68.3 Å / Num. obs: 19124 / % possible obs: 83.5 % / Observed criterion σ(I): 3 / Redundancy: 4.57 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.22 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.2 / % possible all: 41.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VEF Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.73 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 2.237 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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