+Open data
-Basic information
Entry | Database: PDB / ID: 8ucx | |||||||||
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Title | Dihydrofolate Reductase Complexed with Folate | |||||||||
Components | Dihydrofolate reductase | |||||||||
Keywords | OXIDOREDUCTASE / wild-type / folate / DHFR | |||||||||
Function / homology | Function and homology information dihydrofolate metabolic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | |||||||||
Authors | Fried, S.D.E. / Boxer, S.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase Authors: Fried, S.D.E. / Mukherjee, S. / Mao, Y. / Boxer, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ucx.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ucx.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ucx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ucx_validation.pdf.gz | 720.3 KB | Display | wwPDB validaton report |
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Full document | 8ucx_full_validation.pdf.gz | 721 KB | Display | |
Data in XML | 8ucx_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 8ucx_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/8ucx ftp://data.pdbj.org/pub/pdb/validation_reports/uc/8ucx | HTTPS FTP |
-Related structure data
Related structure data | 8vz4C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18067.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA / Plasmid: pET22b-ecDHFR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TR70 | ||||
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#2: Chemical | ChemComp-FOL / | ||||
#3: Chemical | #4: 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: 2.5 Å3/Da / Density % sol: 50.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Mixed 1 microliter of ecDHFR-FOL in 20 mM imidazole at pH 7.0 with 1 microliter of a reservoir solution containing 14%(w/v) PEG 6000, 300 mM MnCl2, and 20 mM imidazole at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 25, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→36.91 Å / Num. obs: 25931 / % possible obs: 99.8 % / Redundancy: 25.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.023 / Rrim(I) all: 0.118 / Χ2: 0.93 / Net I/σ(I): 17.6 / Num. measured all: 658288 |
Reflection shell | Resolution: 1.57→1.59 Å / % possible obs: 95.3 % / Redundancy: 20 % / Rmerge(I) obs: 1.743 / Num. measured all: 23924 / Num. unique obs: 1199 / CC1/2: 0.721 / Rpim(I) all: 0.385 / Rrim(I) all: 1.787 / Χ2: 0.75 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→36.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→36.91 Å
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Refine LS restraints |
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LS refinement shell |
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