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Yorodumi- PDB-4urg: Crystal Structure of GGDEF domain from T.maritima (active-like dimer) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4urg | ||||||
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Title | Crystal Structure of GGDEF domain from T.maritima (active-like dimer) | ||||||
Components | DIGUANYLATE CYCLASE | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Deepthi, A. / Liew, C.W. / Liang, Z.X. / Swaminathan, K. / Lescar, J. | ||||||
Citation | Journal: Plos One / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4urg.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4urg.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 4urg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/4urg ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4urg | HTTPS FTP |
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-Related structure data
Related structure data | 4urqC 4ursC 3iclS C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.93632, 0.20937, 0.28192), Vector: |
-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.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X2A8 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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