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Yorodumi- PDB-3l2b: Crystal structure of the CBS and DRTGG domains of the regulatory ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l2b | ||||||
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Title | Crystal structure of the CBS and DRTGG domains of the regulatory region of Clostridium perfringens pyrophosphatase complexed with activator, diadenosine tetraphosphate | ||||||
Components | Probable manganase-dependent inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / Clostridium perfringens / family II / Inorganic / pyrophosphatase / CBS domain / Bateman domain / AP4A / Diadenosine polyphosphate / DRTGG | ||||||
Function / homology | Function and homology information inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / cobalt ion binding / AMP binding / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Tuominen, H. / Salminen, A. / Oksanen, E. / Jamsen, J. / Heikkila, O. / Lehtio, L. / Magretova, N.N. / Goldman, A. / Baykov, A.A. / Lahti, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structures of the CBS and DRTGG Domains of the Regulatory Region of Clostridiumperfringens Pyrophosphatase Complexed with the Inhibitor, AMP, and Activator, Diadenosine Tetraphosphate. Authors: Tuominen, H. / Salminen, A. / Oksanen, E. / Jamsen, J. / Heikkila, O. / Lehtio, L. / Magretova, N.N. / Goldman, A. / Baykov, A.A. / Lahti, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l2b.cif.gz | 195.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l2b.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 3l2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/3l2b ftp://data.pdbj.org/pub/pdb/validation_reports/l2/3l2b | HTTPS FTP |
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-Related structure data
Related structure data | 3l31SC 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
#1: Protein | Mass: 26974.965 Da / Num. of mol.: 2 / Fragment: regulatory region (UNP residues 66-306) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: str. 13 / Gene: CPE2055 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8XIQ9, inorganic diphosphatase #2: Chemical | ChemComp-B4P / | #3: 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: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 4000, 100mM Tris/HCl pH 8.5, 200mM LiSO4, 0.25mM Ap4A, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97926 Å |
Detector | Type: ADSC Quantum Q315r / Detector: CCD / Date: Apr 27, 2008 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→20 Å / Num. all: 24554 / Num. obs: 24554 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 55.681 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 19.78 |
Reflection shell | Resolution: 2.31→2.44 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.6 / Num. measured obs: 25817 / Num. unique all: 3736 / Num. unique obs: 3736 / Rsym value: 0.374 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L31 Resolution: 2.27→19.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0 / SU B: 16.299 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.08 Å2 / Biso mean: 45.19 Å2 / Biso min: 28.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.27→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.273→2.331 Å / Total num. of bins used: 20
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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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