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- PDB-7dp5: Crystal structure of mutant V45A Brugia malayi thymidylate syntha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dp5 | ||||||
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Title | Crystal structure of mutant V45A Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / THYMIDYLATE SYNTHASE / NUCLEOTIDE SYNTHASE / METHYLTRANSFERASE | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / dihydrofolate reductase activity / methylation / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Keyunratsami, K. / Nualnoi, T. / Wongkamchai, S. / Songsiriritthigul, C. / Chen, C.-J. / Canyuk, B. | ||||||
![]() | ![]() Title: Crystallographic investigation and inhibition of Brugia malayi thymidylate synthase by a folate analog Authors: Keyunratsami, K. / Nualnoi, T. / Wongkamchai, S. / Songsiriritthigul, C. / Chen, C.-J. / Canyuk, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 58.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dp4C ![]() 7dp6C ![]() 1hvyS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34494.387 Da / Num. of mol.: 1 / Mutation: V45A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Bma-tyms-1.1, BM_BM7277 / Plasmid: PQE-30 XA / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 259 molecules ![](data/chem/img/UMP.gif)
![](data/chem/img/MTX.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MTX.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UMP / | ||||
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#3: Chemical | ChemComp-MTX / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.9 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 12, 2013 / Details: DCM |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 53607 / % possible obs: 99.9 % / Redundancy: 4.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.023 / Rrim(I) all: 0.049 / Net I/σ(I): 34.73 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.61 / Num. unique obs: 5288 / CC1/2: 0.809 / CC star: 0.946 / Rpim(I) all: 0.259 / Rrim(I) all: 0.552 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HVY Resolution: 1.6→23.754 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.369 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.071 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.215 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→23.754 Å
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Refine LS restraints |
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LS refinement shell |
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