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Yorodumi- PDB-3mr7: Crystal Structure of Adenylate/Guanylate Cyclase/Hydrolase from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mr7 | ||||||
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Title | Crystal Structure of Adenylate/Guanylate Cyclase/Hydrolase from Silicibacter pomeroyi | ||||||
Components | Adenylate/guanylate cyclase/hydrolase, alpha/beta fold family | ||||||
Keywords | HYDROLASE / alpha-beta fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information cyclic nucleotide biosynthetic process / hydrolase activity / intracellular signal transduction Similarity search - Function | ||||||
Biological species | Ruegeria pomeroyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Adenylate/Guanylate Cyclase/Hydrolase from Silicibacter pomeroyi Authors: Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mr7.cif.gz | 212.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mr7.ent.gz | 179.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/3mr7 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/3mr7 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21440.521 Da / Num. of mol.: 3 / Fragment: residues 2-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPO3024 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q5LP28 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Di-sodium tartrate, 20 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 19470 / Num. obs: 19470 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.7 % / Biso Wilson estimate: 55.64 Å2 / Rsym value: 0.087 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 18.7 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 945 / Rsym value: 0.769 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→45.549 Å / SU ML: 0.36 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0.32 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.827 Å2 / ksol: 0.345 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→45.549 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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