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- PDB-5vis: 1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Syn... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vis | ||||||
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Title | 1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium. | ||||||
![]() | Dihydropteroate Synthase | ||||||
![]() | HYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dihydropteroate Synthase | ||||||
Function / homology | Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : / MALONIC ACID / D(-)-TARTARIC ACID![]() | ||||||
Biological species | soil metagenome (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Wawrzak, Z. / Di Leo, R. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium. Authors: Minasov, G. / Wawrzak, Z. / Di Leo, R. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.7 KB | Display | ![]() |
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PDB format | ![]() | 194.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1aj2S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29726.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) soil metagenome (others) / Plasmid: pMCSG7 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 635 molecules ![](data/chem/img/MLA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/TAR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/TAR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MLA / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-K / |
#5: Chemical | ChemComp-TAR / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 52.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 30.0 mg/ml, 0.25M Sodium chloride, 0.25M Potassium chloride, 0.01M HEPES (pH 7.5); Screen: 0.2M Potassium citrate, 0.1M MES (pH 6.5), 20% (w/v) PEG 3350; Cryo: 5% (v/v) PEG 200, paratone. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 66663 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rsym value: 0.072 / Χ2: 1.027 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3260 / CC1/2: 0.737 / Rpim(I) all: 0.325 / Rsym value: 0.752 / Χ2: 1.032 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AJ2 Resolution: 1.73→29.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.612 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.277 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→29.99 Å
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Refine LS restraints |
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