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Yorodumi- PDB-7dp6: Crystal structure of mutant V45T Brugia malayi thymidylate syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dp6 | ||||||
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Title | Crystal structure of mutant V45T Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / THYMIDYLATE SYNTHASE / NUCLEOTIDE SYNTHASE / METHYLTRANSFERASE | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / dihydrofolate reductase activity / methylation / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Brugia malayi (agent of lymphatic filariasis) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Keyunratsami, K. / Nualnoi, T. / Wongkamchai, S. / Songsiriritthigul, C. / Chen, C.-J. / Canyuk, B. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dp6.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dp6.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 7dp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dp6_validation.pdf.gz | 800.8 KB | Display | wwPDB validaton report |
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Full document | 7dp6_full_validation.pdf.gz | 804.8 KB | Display | |
Data in XML | 7dp6_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7dp6_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/7dp6 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/7dp6 | HTTPS FTP |
-Related structure data
Related structure data | 7dp4C 7dp5C 1hvyS 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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Unit cell |
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-Components
#1: Protein | Mass: 34524.414 Da / Num. of mol.: 1 / Mutation: V45T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis) Gene: Bma-tyms-1.1, BM_BM7277 / Plasmid: PQE-30 XA / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 [PREP4] / References: UniProt: A0A4E9EZW9, thymidylate synthase | ||||||
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#2: Chemical | ChemComp-UMP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.77 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl, 20 mM betamercaptoethanol, 8%(w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / 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: 1.85→30 Å / Num. obs: 34055 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.014 / Rrim(I) all: 0.031 / Net I/σ(I): 51.2 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.47 / Num. unique obs: 3402 / CC1/2: 0.876 / CC star: 0.966 / Rpim(I) all: 0.257 / Rrim(I) all: 0.56 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HVY Resolution: 1.85→24.679 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.648 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.108 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: 40.835 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→24.679 Å
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Refine LS restraints |
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LS refinement shell |
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