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Yorodumi- PDB-5o25: Structure of wildtype T.maritima PDE (TM1595) in ligand-free state -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o25 | |||||||||
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Title | Structure of wildtype T.maritima PDE (TM1595) in ligand-free state | |||||||||
Components | TmPDE | |||||||||
Keywords | HYDROLASE / phosphodiesterase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Witte, G. / Drexler, D. / Mueller, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Structure / Year: 2017 Title: Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima. Authors: Drexler, D.J. / Muller, M. / Rojas-Cordova, C.A. / Bandera, A.M. / Witte, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o25.cif.gz | 275.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o25.ent.gz | 222 KB | Display | PDB format |
PDBx/mmJSON format | 5o25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o25_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 5o25_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 5o25_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5o25_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/5o25 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o25 | HTTPS FTP |
-Related structure data
Related structure data | 5o1uSC 5o4zC 5o58C 5o70C 5o7fC 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37870.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1595 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1T1 |
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-Non-polymers , 5 types, 543 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | #6: 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: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG4000 0.1M Tris pH7.5 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→95 Å / Num. obs: 73632 / % possible obs: 96.5 % / Redundancy: 6.9 % / Rrim(I) all: 0.117 / Net I/σ(I): 13.34 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.01 / Num. unique obs: 5359 / CC1/2: 0.66 / Rrim(I) all: 1.018 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O1U Resolution: 1.75→19.311 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.311 Å
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Refine LS restraints |
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LS refinement shell |
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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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