+Open data
-Basic information
Entry | Database: PDB / ID: 1dus | ||||||
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Title | MJ0882-A hypothetical protein from M. jannaschii | ||||||
Components | MJ0882 | ||||||
Keywords | STRUCTURAL GENOMICS / Hypothetical protein / Methanococcus jannaschii / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Hung, L. / Huang, L. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2002 Title: Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii Authors: Huang, L. / Hung, L. / Odell, M. / Yokota, H. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dus.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dus.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/1dus ftp://data.pdbj.org/pub/pdb/validation_reports/du/1dus | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21945.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Production host: Escherichia coli (E. coli) / References: UniProt: Q58292 |
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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: 1.99 Å3/Da / Density % sol: 38.05 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.13 Details: 2.75 M ammonium sulfate, 0.1 M MES, pH 5.13, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9797 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 23830 / Num. obs: 23819 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 8 % / Rmerge(I) obs: 0.32 / Num. unique all: 1153 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Resolution: 1.8→19.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 543599.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.36 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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