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Yorodumi- PDB-1l5z: CRYSTAL STRUCTURE OF THE E121K SUBSTITUTION OF THE RECEIVER DOMAI... -
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-Basic information
Entry | Database: PDB / ID: 1l5z | ||||||
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Title | CRYSTAL STRUCTURE OF THE E121K SUBSTITUTION OF THE RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD | ||||||
Components | C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD | ||||||
Keywords | TRANSCRIPTION REGULATOR / two component receiver domain / sigma 54 / regulator of AAA+ ATPase | ||||||
Function / homology | Function and homology information phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Park, S. / Meyer, M. / Jones, A.D. / Yennawar, H.P. / Yennawar, N.H. / Nixon, B.T. | ||||||
Citation | Journal: FASEB J. / Year: 2002 Title: Two-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain Authors: Park, S. / Meyer, M. / Jones, A.D. / Yennawar, H.P. / Yennawar, N.H. / Nixon, B.T. #1: Journal: FASEB J. / Year: 2001 Title: A dimeric two-component receiver domain inhibits the sigma54-dependent ATPase in DctD Authors: Meyer, M.G. / Park, S. / Zeringue, L. / Staley, M. / McKinstry, M. / Kaufman, R.I. / Zhang, H. / Yan, D. / Yennawar, N. / Yennawar, H. / Farber, G.K. / Nixon, B.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l5z.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l5z.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 1l5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/1l5z ftp://data.pdbj.org/pub/pdb/validation_reports/l5/1l5z | HTTPS FTP |
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-Related structure data
Related structure data | 1l5yC 1qkkS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | analytical ultracentrifuge data indicates solution form is a dimer; genetic and biochemical data indicates substitution destabilizes the dimer ~20-fold, leading to 'derepression' of the ATPase domain asymmetric unit is a monomer biological unit is a dimer - build with symmetry operation -X, -Y, Z |
-Components
#1: Protein | Mass: 16821.326 Da / Num. of mol.: 1 / Fragment: RECEIVER DOMAIN, RESIDUES 2-143 / Mutation: E121K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: dctD / Plasmid: pT143E121K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/De3/pLysS / References: UniProt: P13632 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-GOL / #4: 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: 4.17 Å3/Da / Density % sol: 70.47 % | |||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, lithium sulfate, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2001 / Details: MSC Blue Confocal Optical System |
Radiation | Monochromator: MSC Blue Confocal Optical System / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.7 Å / Num. all: 19264 / Num. obs: 19264 / % possible obs: 98.6 % / Observed criterion σ(I): 2.2 / Redundancy: 3.04 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.61 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3548 / % possible all: 97.5 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 98.9 % / Num. measured all: 59135 |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QKK Resolution: 2→36.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 215180.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.2093 Å2 / ksol: 0.385197 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 9.7 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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