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- PDB-4urq: Crystal Structure of GGDEF domain (I site mutant) from T.maritima -
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Open data
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Basic information
Entry | Database: PDB / ID: 4urq | ||||||
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Title | Crystal Structure of GGDEF domain (I site mutant) from T.maritima | ||||||
![]() | DIGUANYLATE CYCLASE![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deepthi, A. / Liew, C.W. / Liang, Z.X. / Swamianthan, K. / Lescar, J. | ||||||
![]() | ![]() Title: Structure of a Diguanylate Cyclase from Thermotoga Maritima: Insights Into Activation, Feedback Inhibition and Thermostability Authors: Deepthi, A. / Liew, C.W. / Liang, Z.X. / Kunchithapadam, S. / Lescar, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.1 KB | Display | ![]() |
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PDB format | ![]() | 157.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4urgC ![]() 4ursC ![]() 3iclS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 19487.449 Da / Num. of mol.: 6 / Fragment: GGDEF DOMAIN, RESIDUES 81-248 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow![]() | Details: 2 M NACL, 10% (W/V) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→58.97 Å / Num. obs: 43759 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 58.14 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3ICL Resolution: 2.5→38.37 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9122 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.258
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Displacement parameters | Biso mean: 53.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.374 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→38.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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