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- PDB-4urg: Crystal Structure of GGDEF domain from T.maritima (active-like dimer) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4urg | ||||||
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Title | Crystal Structure of GGDEF domain from T.maritima (active-like dimer) | ||||||
![]() | DIGUANYLATE CYCLASE | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deepthi, A. / Liew, C.W. / Liang, Z.X. / Swaminathan, 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 | ![]() | 80.3 KB | Display | ![]() |
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PDB format | ![]() | 61.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4urqC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.93632, 0.20937, 0.28192), Vector: |
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Components
#1: Protein | Mass: 19580.516 Da / Num. of mol.: 2 / Fragment: GGDEF DOAMIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % / Description: NONE |
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Crystal grow | pH: 4 Details: 0.15 M LITHIUM SULFATE, 0.1 M CITRIC ACID (PH 4.0), 10% (W/V) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→36.49 Å / Num. obs: 27197 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 6.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ICL Resolution: 1.9→22.71 Å / Cor.coef. Fo:Fc: 0.9266 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.162 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.146
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Displacement parameters | Biso mean: 25.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.236 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→22.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 14
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