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- PDB-3kkz: Crystal structure of the Q5LES9_BACFN protein from Bacteroides fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kkz | ||||||
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Title | Crystal structure of the Q5LES9_BACFN protein from Bacteroides fragilis. Northeast Structural Genomics Consortium Target BfR250. | ||||||
![]() | uncharacterized protein Q5LES9 | ||||||
![]() | TRANSFERASE / putative methyltransferase / BFR250 / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYLMETHIONINE / Methyltransf_25 domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the Q5LES9_BACFN protein from Bacteroides fragilis. Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.7 KB | Display | ![]() |
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PDB format | ![]() | 194.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 971.4 KB | Display | ![]() |
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Full document | ![]() | 977.7 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | monomer according to aggregation screening |
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Components
#1: Protein | Mass: 30907.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25285/NCTC 9343 / Gene: BF1671 / Plasmid: pET 21-23C / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 293 K / Method: microbatch under paraffin oil / pH: 5.6 Details: 25% PEG 4000, 0.17M ammonium acetate, 0.085M sodium citrate, 15% glycerol, 3mM SAM, pH 5.6, Microbatch under paraffin oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97909 Å / Relative weight: 1 |
Reflection | Resolution: 1.677→50 Å / Num. all: 122912 / Num. obs: 122052 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 4.2 / % possible all: 87.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.221 Å2 / ksol: 0.399 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.677→34.714 Å
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Refine LS restraints |
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LS refinement shell |
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