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Yorodumi- PDB-4dzr: The crystal structure of protein-(glutamine-N5) methyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dzr | ||||||
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Title | The crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 | ||||||
Components | Protein-(Glutamine-N5) methyltransferase, release factor-specific | ||||||
Keywords | TRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Function and homology information peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / nucleic acid binding / metal ion binding Similarity search - Function | ||||||
Biological species | Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.551 Å | ||||||
Authors | Tan, K. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 Authors: Tan, K. / Chhor, G. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dzr.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dzr.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 4dzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dzr_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 4dzr_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 4dzr_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4dzr_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/4dzr ftp://data.pdbj.org/pub/pdb/validation_reports/dz/4dzr | HTTPS FTP |
-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 on special symmetry positions |
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Details | Experimentally unknown. It is predicted the molecule is a monomer. |
-Components
#1: Protein | Mass: 23795.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 (bacteria) Strain: subsp. acidocaldarius DSM 446 / Gene: Aaci_2779 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C8WUG7 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS STATE THAT THE EXPRESSED PROTEIN WAS A FULL LENGTH PROTEIN WITH SEQUENCE: SNA(MSE) ...THE AUTHORS STATE THAT THE EXPRESSED PROTEIN WAS A FULL LENGTH PROTEIN WITH SEQUENCE: SNA(MSE)SEAKYFVARL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M calcium acetate hydrate, pH 7.5, 20% (w/v) PEG 3350, 0.0125mg/ml Trypsin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931, 0.97948 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012 / Details: mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.55→31 Å / Num. all: 8235 / Num. obs: 8235 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.8 | |||||||||
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.2 / Num. unique all: 403 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.551→30.883 Å / SU ML: 0.82 / σ(F): 1.35 / Phase error: 26.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.155 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.551→30.883 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.241 Å / Origin y: 14.54 Å / Origin z: 15.4956 Å
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Refinement TLS group | Selection details: chain A |