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Yorodumi- PDB-3f4k: Crystal structure of a probable methyltransferase from Bacteroide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f4k | ||||||
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Title | Crystal structure of a probable methyltransferase from Bacteroides thetaiotaomicron. Northeast Structural Genomics target BtR309. | ||||||
Components | Putative methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Seetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a probable methyltransferase from Bacteroides thetaiotaomicron. Northeast Structural Genomics target BtR309. Authors: Seetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f4k.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f4k.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 3f4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/3f4k ftp://data.pdbj.org/pub/pdb/validation_reports/f4/3f4k | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29489.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_2972, OrderedLocusNames / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A3I2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 170mM Ammonium Acetate, 85mM Na Citrate pH 5.6, 15% glycerol, 25.5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 26321 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.068 / Net I/σ(I): 15 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 9.8 / Rsym value: 0.258 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→42.41 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 98986.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5887 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→42.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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