+Open data
-Basic information
Entry | Database: PDB / ID: 5m1t | ||||||
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Title | PaMucR Phosphodiesterase, c-di-GMP complex | ||||||
Components | MucR Phosphodiesterase | ||||||
Keywords | SIGNALING PROTEIN / EAL domain Phosphodiesterase | ||||||
Function / homology | Function and homology information cyclic-guanylate-specific phosphodiesterase activity / diguanylate cyclase activity / cellular response to nitric oxide / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Hutchin, A. / Tews, I. / Walsh, M.A. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases. Authors: Bellini, D. / Horrell, S. / Hutchin, A. / Phippen, C.W. / Strange, R.W. / Cai, Y. / Wagner, A. / Webb, J.S. / Tews, I. / Walsh, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m1t.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m1t.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/5m1t ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m1t | HTTPS FTP |
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-Related structure data
Related structure data | 4y9mC 5mf5C 5mfuC 5mkgC 2r6oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 448 - 680 / Label seq-ID: 44 - 276
NCS ensembles :
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-Components
#1: Protein | Mass: 30815.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA1727 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I310 #2: Chemical | #3: Chemical | ChemComp-MG / #4: 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: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.055M MES, 0.045M Imidazole, 12.5% PEG 1000, 12.5% PEG3350, 12.5% MPD, 0.03M diethyleneglycol, 0.03M triethyleneglycol, 0.03M tetraethyleneglycol, 0.03M pentaethyleneglycol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2014 | |||||||||||||||||||||
Radiation | Monochromator: Double crystal Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.27→45.27 Å / Num. obs: 24883 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.167 / Net I/σ(I): 11.3 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2R6O Resolution: 2.27→45.27 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.506 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.223 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.452 Å2
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Refinement step | Cycle: 1 / Resolution: 2.27→45.27 Å
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Refine LS restraints |
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