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Yorodumi- PDB-1bc5: CHEMOTAXIS RECEPTOR RECOGNITION BY PROTEIN METHYLTRANSFERASE CHER -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bc5 | ||||||
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Title | CHEMOTAXIS RECEPTOR RECOGNITION BY PROTEIN METHYLTRANSFERASE CHER | ||||||
Components |
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Keywords | COMPLEX (METHYLTRANSFERASE/PEPTIDE) / METHYLTRANSFERASE / PEPTIDE BINDING / CHEMOTAXIS RECEPTOR / COMPLEX (METHYLTRANSFERASE-PEPTIDE) / COMPLEX (METHYLTRANSFERASE-PEPTIDE) complex | ||||||
Function / homology | Function and homology information protein-glutamate O-methyltransferase / protein-glutamate O-methyltransferase activity / chemotaxis / methylation Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Djordjevic, S. / Stock, A.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Chemotaxis receptor recognition by protein methyltransferase CheR. Authors: Djordjevic, S. / Stock, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bc5.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bc5.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 1bc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bc5 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bc5 | HTTPS FTP |
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-Related structure data
Related structure data | 1af7S S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 30992.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PME43 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P07801, protein-glutamate O-methyltransferase |
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#2: Protein/peptide | Mass: 721.757 Da / Num. of mol.: 1 Fragment: C-TERMINAL PENTAPEPTIDE, ACETYLATED ASN-TRP-GLU-THR-PHE Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CO / |
#4: Chemical | ChemComp-SAH / |
#5: 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: 2.55 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: PROTEIN WAS CRYSTALLIZED FROM 30 % PEG 5000 MME, 25 MM IMIDAZOLE PH 6.8, 15 MM COCL2, 1MM BETA-MERCAPTOETHANOL. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 263 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→23 Å / Num. obs: 16682 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.28 / % possible all: 89 |
Reflection | *PLUS Num. measured all: 52170 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 89 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AF7 Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.204 / % reflection Rfree: 5 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.288 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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