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Yorodumi- PDB-1jbm: Heptameric crystal structure of Mth649, an Sm-like archaeal prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jbm | ||||||
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Title | Heptameric crystal structure of Mth649, an Sm-like archaeal protein from Methanobacterium thermautotrophicum | ||||||
Components | PUTATIVE SNRNP SM-LIKE PROTEIN | ||||||
Keywords | STRUCTURAL GENOMICS / ring-shaped homoheptamer / all beta-strand | ||||||
Function / homology | Function and homology information Sm-like protein family complex / intracellular organelle / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Mura, C. / Eisenberg, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) Authors: Mura, C. / Kozhukhovsky, A. / Gingery, M. / Phillips, M. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jbm.cif.gz | 119.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jbm.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jbm ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jbm | HTTPS FTP |
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-Related structure data
Related structure data | 1jriC 1lnxC 1lojC 1i8fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the homoheptameric ring found in the asymmetric unit (P1 cell). There are no additional symmetry transformations. |
-Components
#1: Protein | Mass: 9573.998 Da / Num. of mol.: 7 / Fragment: full-length Sm protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: Mth0649 ORF / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26745 #2: Chemical | ChemComp-ACY / #3: Chemical | ChemComp-EDO / #4: 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: 2.14 Å3/Da / Density % sol: 42.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG-4000, acetate, citrate buffer, NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2001 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→90 Å / Num. all: 44472 / Num. obs: 44472 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.14 / % possible all: 67.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I8F Resolution: 1.85→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.4 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.92 Å
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