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Yorodumi- PDB-6uwq: Crystal structure of dihydrofolate reductase from Mycobacterium u... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uwq | ||||||
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Title | Crystal structure of dihydrofolate reductase from Mycobacterium ulcerans with SDDC-0001565 inhibitor | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / DHFR / Structure-guided Drug Discovery Coalition / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding Similarity search - Function | ||||||
Biological species | Mycobacterium ulcerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: to be published Title: Crystal structure of dihydrofolate reductase from Mycobacterium ulcerans with SDDC-0001565 inhibitor Authors: Mayclin, S.J. / Abendroth, J.A. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uwq.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uwq.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 6uwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uwq_validation.pdf.gz | 421.9 KB | Display | wwPDB validaton report |
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Full document | 6uwq_full_validation.pdf.gz | 422.2 KB | Display | |
Data in XML | 6uwq_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6uwq_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/6uwq ftp://data.pdbj.org/pub/pdb/validation_reports/uw/6uwq | HTTPS FTP |
-Related structure data
Related structure data | 6uwwC 1df7S 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: 19035.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria) Strain: Agy99 / Gene: dfrA, MUL_2179 / Plasmid: MyulA.01062.a.B13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PQG8, dihydrofolate reductase | ||||
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#2: Chemical | ChemComp-NAP / | ||||
#3: Chemical | ChemComp-QKJ / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.75 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MyulA.01062.a.B13.PS38558 at 7.98mg/ml, incubated with 3 mM SDDC-0001565 and 3 mM NADP, mixed 1:1 with 100mM Bis-Tris:HCl pH6.5, 25% (w/v) PEG3350, 7.98mg/mL MyulA.01062.a.B13.PS38558. Tray: ...Details: MyulA.01062.a.B13.PS38558 at 7.98mg/ml, incubated with 3 mM SDDC-0001565 and 3 mM NADP, mixed 1:1 with 100mM Bis-Tris:HCl pH6.5, 25% (w/v) PEG3350, 7.98mg/mL MyulA.01062.a.B13.PS38558. Tray: 311137d2, puck: sxq1-11, cryoprotected with 20% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 21600 / % possible obs: 98.3 % / Redundancy: 3.701 % / Biso Wilson estimate: 21.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Χ2: 0.984 / Net I/σ(I): 21.55 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1df7 Resolution: 1.5→35.38 Å / SU ML: 0.2018 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.6561
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→35.38 Å
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Refine LS restraints |
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LS refinement shell |
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