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- PDB-1qkk: Crystal structure of the receiver domain and linker region of Dct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qkk | ||||||
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Title | Crystal structure of the receiver domain and linker region of DctD from Sinorhizobium meliloti | ||||||
![]() | C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN | ||||||
![]() | TRANSCRIPTIONAL REGULATORY PROTEIN / RECEIVER DOMAIN / 2-COMPONENT SIGNAL TRANSDUCTION / SIGMA-54 DEPENDENT TRANSCRIPTIONAL ACTIVATOR / BACTERIAL ENHANCER BINDING PROTEIN / HIGH SOLVENT CONTENT CRYSTAL | ||||||
Function / homology | ![]() phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meyer, M.G. / Park, S. / Zeringue, L. / Staley, M. / Mckinstry, M. / Kaufman, R.I. / Zhang, H. / Yan, D. / Yennawar, N. / Farber, G.K. / Nixon, B.T. | ||||||
![]() | ![]() 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. #1: Journal: Science / Year: 1987 Title: Crystallographic R Factor Refinement by Molecular Dynamics Authors: Brunger, A.T. / Kuriyan, J. / Karplus, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.4 KB | Display | ![]() |
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PDB format | ![]() | 31.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.1 KB | Display | ![]() |
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Full document | ![]() | 366.6 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE MOLECULE EXISTS AS A DIMER IN SOLUTION . THE DIMER ISCOMPRISED OF MONOMERS FROM DIFFERENT UNIT CELLS.DIMERIZATION SURFACES OCCUR AT THE FACES OF THE UNIT CELL"BOX". |
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Components
#1: Protein | Mass: 16821.260 Da / Num. of mol.: 1 / Fragment: RESIDUES 2 TO 143, RECEIVER DOMAIN Source method: isolated from a genetically manipulated source Details: THE PROTEIN WAS EXPRESSED WITH THE C-TERMINAL HIS-TAG, KLAAALEHHHHHH. COORDINATES ARE SUBMITTED ONLY FOR THE MONOMER, WHICH COMPRISES THE COMPLETE ASYMMETRIC UNIT. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Compound details | CHAIN A: RESIDUES 144 TO 156 ARE A HIS TAG |
Source details | THE PROTEIN IS FROM N.A. STRAIN=1021 REFERENCE: JIANG J., GU B., ALBRIGHT L.M., NIXON B.T., ...THE PROTEIN IS FROM N.A. STRAIN=1021 REFERENCE: JIANG J., GU B., ALBRIGHT L.M., NIXON B.T., CONSERVATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71 % Description: DATA WERE COLLECTED AT BEAMLINE 17-ID (OR 17-BM) IN THE FACILITIES OF THEINDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION COLLABORATIVE ACCESS TEAM (IMCA-CAT) AT THE ADVANCED PHOTON ...Description: DATA WERE COLLECTED AT BEAMLINE 17-ID (OR 17-BM) IN THE FACILITIES OF THEINDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION COLLABORATIVE ACCESS TEAM (IMCA-CAT) AT THE ADVANCED PHOTON SOURCE.THESE FACILITIES ARE SUPPORTED BY THE COMPANIES OF THE INDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION THROUGH A CONTRACT WITH ILLINOIS INSTITUTE OF TECHNOLOGY (IIT), EXECUTED THROUGH THE IIT'S CENTER FOR SYNCHROTRON RADIATION RESEARCH AND INSTRUMENTATION. | ||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 50 MM NA SUCCINATE PH 5.6, 70 MM AMMONIUM PHOSPHATE MONOBASIC, 1 MM DTT | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / 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: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 27, 1998 / Details: NO FOCUSSING MIRROR | ||||||||||||
Radiation | Monochromator: CRYOGENICALLY COOLED SI (111) MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→20 Å / Num. obs: 61207 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.062 / Net I/σ(I): 34 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.324 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Num. obs: 32439 / % possible obs: 86.1 % / Rmerge(I) obs: 0.059 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.1063 Å2 / ksol: 0.415432 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.231 / Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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