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Yorodumi- PDB-2bde: Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bde | ||||||
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Title | Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1 | ||||||
Components | cytosolic IMP-GMP specific 5'-nucleotidase | ||||||
Keywords | DNA BINDING PROTEIN / alpha beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information 5'-nucleotidase activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Ho, C.K. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1 Authors: Forouhar, F. / Abashidze, M. / Ho, C.K. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bde.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bde.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bde_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 2bde_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 2bde_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 2bde_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/2bde ftp://data.pdbj.org/pub/pdb/validation_reports/bd/2bde | HTTPS FTP |
-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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 55158.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: 3078646 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-Gold+Magic / References: UniProt: Q5ZZB6 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.97 Å3/Da / Density % sol: 75.23 % Description: Reflections reported in data collection include friedel pairs |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.15 Details: 100mM MES, 20% PEG400, 100mM KBr, 5mM DTT, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898, 0.97943, 0.96795 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2005 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→30.12 Å / Num. all: 44284 / Num. obs: 44284 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.9 % / Biso Wilson estimate: 70.2 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.081 / Net I/σ(I): 29 | ||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 10.93 / Num. unique all: 2447 / Rsym value: 0.285 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→30.12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 475983.63 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs have been used in refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.9387 Å2 / ksol: 0.302233 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→30.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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