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Yorodumi- PDB-8f82: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f82 | |||||||||
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Title | Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor MAM845 | |||||||||
Components | Dihydrofolate reductase | |||||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | |||||||||
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 / Resolution: 1.2 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor MAM845 Authors: Liu, L. / Battaile, K.P. / Lovell, S. / Staker, B.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f82.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f82.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 8f82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f82_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8f82_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8f82_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 8f82_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/8f82 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/8f82 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19035.619 Da / Num. of mol.: 1 / Fragment: MyulA.01062.a.B13 / Mutation: C89S/E96A Source method: isolated from a genetically manipulated source Details: MAHHHHHHMTSVGLIWAQSTSGVIGRDGGIPWRLPEDLAHFKRLTMGHTVVMGRRTWDSLPAAHRPLPGRRNVVVTRQTG LVAHGAQVVGSLEQALSPAEPDAATWVIGGAQIYALALPLANRCEVTEVDVDLPPEDEDALAPVLDQTWAGTSGEWLVSR SGLRYRMHSYRRL Source: (gene. exp.) Mycobacterium ulcerans (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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-Non-polymers , 5 types, 200 molecules
#2: Chemical | ChemComp-XJT / |
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#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-NAP / |
#5: Chemical | ChemComp-BR / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus B4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI, MyulA.01062.a.B13.PS38558 at 10 mg/mL. Tray: ...Details: Morpheus B4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI, MyulA.01062.a.B13.PS38558 at 10 mg/mL. Tray: Tray358B4 MAM777, Puck: PUCK HR00407 pin15, Cryo: Direct |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Sep 22, 2022 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→44.02 Å / Num. obs: 47045 / % possible obs: 91 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.015 / Rrim(I) all: 0.031 / Χ2: 1.02 / Net I/σ(I): 28.8 / Num. measured all: 193506 |
Reflection shell | Resolution: 1.2→1.23 Å / % possible obs: 44.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.128 / Num. measured all: 4307 / Num. unique obs: 1711 / CC1/2: 0.971 / Rpim(I) all: 0.096 / Rrim(I) all: 0.161 / Χ2: 0.96 / Net I/σ(I) obs: 7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→44.02 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→44.02 Å
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Refine LS restraints |
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LS refinement shell |
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