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- PDB-1m5u: CRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK. STRUCTURE AT PH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m5u | ||||||
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Title | CRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK. STRUCTURE AT PH 8.0 IN THE APO-FORM | ||||||
![]() | cell division response regulator DivK | ||||||
![]() | SIGNALING PROTEIN / CELL CYCLE / RESPONSE REGULATOR / SIGNAL TRANSDUCTION PROTEIN / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | ![]() protein histidine kinase activity / cellular hyperosmotic response / phosphorelay signal transduction system / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guillet, V. / Ohta, N. / Cabantous, S. / Newton, A. / Samama, J.-P. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: Crystallographic and biochemical studies of DivK reveal novel features of an essential response regulator in Caulobacter crescentus Authors: Guillet, V. / Ohta, N. / Cabantous, S. / Newton, A. / Samama, J.-P. #1: ![]() Title: Characterization and Crystallization of Divk, an Essential Response Regulator for Cell Division and Differentiation in Caulobacter Crescentus Authors: Cabantous, S. / Guillet, V. / Ohta, N. / Newton, A. / Samama, J.-P. #2: ![]() Title: An Essential Single Domain Response Regulator Required for Normal Cell Division and Differentiation in Caulobacter Crescentus Authors: Hecht, G.B. / Lane, T. / Ohta, N. / Sommer, J.M. / Newton, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.5 KB | Display | ![]() |
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PDB format | ![]() | 24.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.6 KB | Display | ![]() |
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Full document | ![]() | 424.8 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m5tC ![]() 1mavC ![]() 1mb0C ![]() 1mb3C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14059.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: STRUCTURE AT PH 8.0 IN THE APO-FORM / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging or sitting-drop / pH: 8 Details: MES 50mM PH6.0,PEG MME 550 32% At 285K. The Protein was Concentrated At 2 MG/ML In MES-NAOH PH 6.00 (20 mM), DTT (5 mM) And Mixed With An Equal Volume Of The Reservoir Solution Containing ...Details: MES 50mM PH6.0,PEG MME 550 32% At 285K. The Protein was Concentrated At 2 MG/ML In MES-NAOH PH 6.00 (20 mM), DTT (5 mM) And Mixed With An Equal Volume Of The Reservoir Solution Containing PEG MME 550 (32%), MES PH 6.00 (40 mM), DTT (5mM). Crystal Size (300X40X40 microM3) In 20microL Sitting Drops. VAPOR DIFFUSION, HANGING OR SITTING-DROP at 285K. Crystals Were Transferred In Reservoir Solutions Whose Ph Was Increased From 6.0 To 8.0 By Steps Of 0.5 Ph Units (The Soaking Time In Each Solution Was 12 Hours). Crystals Were Frozen In Liquid Propane After Soaking For A Few Seconds In Peg Mme 550 (50%), Tris Ph 8.0 (40 Mm)., pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging dropDetails: Cabantous, S., (2002) Acta Crystallogr., Sect.D, 58, 1249. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: IMAGE PLATE / Date: Apr 17, 2000 |
Radiation | Monochromator: Si111 or Si311 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→35 Å / Num. all: 8414 / Num. obs: 8414 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.87→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 7.9 / Num. unique all: 5050 / % possible all: 94.1 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. measured all: 42648 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 94.1 % / Rmerge(I) obs: 0.097 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: APO-DIVK SOLVED AT PH6 Resolution: 1.87→15 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 111.642 Å2 / ksol: 0.524279 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.22 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.99 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.1901 / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.253 / Rfactor Rwork: 0.184 |