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Yorodumi- PDB-4osg: Klebsiella pneumoniae complexed with NADPH and 6-ethyl-5-[(3R)-3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4osg | ||||||
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Title | Klebsiella pneumoniae complexed with NADPH and 6-ethyl-5-[(3R)-3-[3-methoxyl-5-(pyridine-4-yl)phenyl]but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP1006) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | Oxidoreductase/Oxidoreductase inhibitor / Oxidoreductase / hydride shift / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Klebsiella pneumoniae CG43 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Lamb, K.M. / Anderson, A.C. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2014 Title: Crystal Structures of Klebsiella pneumoniae Dihydrofolate Reductase Bound to Propargyl-Linked Antifolates Reveal Features for Potency and Selectivity. Authors: Lamb, K.M. / Lombardo, M.N. / Alverson, J. / Priestley, N.D. / Wright, D.L. / Anderson, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4osg.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4osg.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 4osg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4osg_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 4osg_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4osg_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 4osg_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/4osg ftp://data.pdbj.org/pub/pdb/validation_reports/os/4osg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 18813.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae CG43 (bacteria) / Gene: folA, D364_00170 / Production host: Escherichia coli (E. coli) / References: UniProt: U5M636, dihydrofolate reductase |
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-Non-polymers , 8 types, 31 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-06U / #4: Chemical | ChemComp-EOH / | #5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PEG / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 2.62 Å3/Da / Density % sol: 53.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100 mM cacodylate pH7.4, 125 mM sodium acetate, 25% (w/v) PEG 8000, 11 mM calcium chloride, 11 mM bentaine hydrochloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2013 |
Radiation | Monochromator: A KOHZU double crystal monochromator with a sagittally focused second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→39.27 Å / Num. all: 20988 / Num. obs: 19813 / % possible obs: 94.4 % / Observed criterion σ(F): 13.4 / Observed criterion σ(I): 13.4 / Redundancy: 1.67 % / Rmerge(I) obs: 0.049 / Rsym value: 0.07 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.468 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→39.27 Å / σ(F): 2.7 / Phase error: 35.41 / Stereochemistry target values: TWIN_LSQ_F
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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: 2.7→39.27 Å
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Refine LS restraints |
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LS refinement shell |
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