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Yorodumi- PDB-1f51: A TRANSIENT INTERACTION BETWEEN TWO PHOSPHORELAY PROTEINS TRAPPED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f51 | ||||||
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Title | A TRANSIENT INTERACTION BETWEEN TWO PHOSPHORELAY PROTEINS TRAPPED IN A CRYSTAL LATTICE REVEALS THE MECHANISM OF MOLECULAR RECOGNITION AND PHOSPHOTRANSFER IN SINGAL TRANSDUCTION | ||||||
Components |
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Keywords | TRANSFERASE / TWO COMPONENT SYSTEM / SINGAL TRANDUCTION / RESPONSE REGULATOR / PHOSPHOTRANSFERASE / SPORULATION / PHOSPHORELAY | ||||||
Function / homology | Function and homology information Transferases; Transferring phosphorus-containing groups / sporulation resulting in formation of a cellular spore / phosphorelay sensor kinase activity / phosphorelay signal transduction system / kinase activity / phosphorylation / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zapf, J. / Sen, U. / Madhusudan, M. / Hoch, J.A. / Varughese, K.I. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Authors: Zapf, J. / Sen, U. / Madhusudan, M. / Hoch, J.A. / Varughese, K.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f51.cif.gz | 251.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f51.ent.gz | 200.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f51 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f51 | HTTPS FTP |
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-Related structure data
-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: 21382.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET20B References: UniProt: P06535, Transferases; Transferring phosphorus-containing groups #2: Protein | Mass: 13575.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET20B References: UniProt: P06628, Transferases; Transferring phosphorus-containing groups #3: Chemical | |
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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: 2.62 Å3/Da / Density % sol: 53.11 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.1 / Details: 0.5M KCL, 24% PEG2K AND ALF3 AT pH8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: PT COATED SI FLAT MIRROR BENT FOR VERTICAL FOCUS |
Radiation | Monochromator: SI BENT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3→45 Å / Num. obs: 29914 / % possible obs: 99 % / Redundancy: 4.1 % / Rsym value: 7.6 / Net I/σ(I): 18 |
Reflection shell | Resolution: 3→3.14 Å / Mean I/σ(I) obs: 3.1 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 122403 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 98.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SRR AND 1IXM Resolution: 3→45 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 503956.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.18 Å2 / ksol: 0.273 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.332 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.309 |