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Yorodumi- PDB-4ohf: Crystal structure of cytosolic nucleotidase II (LPG0095) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ohf | ||||||
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Title | Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with GMP from Legionella pneumophila, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LGR1 | ||||||
Components | Cytosolic IMP-GMP specific 5'-nucleotidase | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / 3-domained structure that resembles HAD / nucleotidase. It catalyzes the breakdown of selected nucleoside monophosphates / cytosol | ||||||
Function / homology | Function and homology information 5'-nucleotidase activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||
Authors | Srinivisan, B. / Forouhar, F. / Shukla, A. / Sampangi, C. / Kulkarni, S. / Abashidze, M. / Seetharaman, J. / Lew, S. / Mao, L. / Acton, T.B. ...Srinivisan, B. / Forouhar, F. / Shukla, A. / Sampangi, C. / Kulkarni, S. / Abashidze, M. / Seetharaman, J. / Lew, S. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.M. / Tong, L. / Balaram, H. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila. Authors: Srinivasan, B. / Forouhar, F. / Shukla, A. / Sampangi, C. / Kulkarni, S. / Abashidze, M. / Seetharaman, J. / Lew, S. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Balaram, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ohf.cif.gz | 376.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ohf.ent.gz | 306.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ohf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ohf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ohf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ohf_validation.xml.gz | 70.6 KB | Display | |
Data in CIF | 4ohf_validation.cif.gz | 95.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/4ohf ftp://data.pdbj.org/pub/pdb/validation_reports/oh/4ohf | HTTPS FTP |
-Related structure data
Related structure data | 4g63SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 54736.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / Gene: lpg0095 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5ZZB6 #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: 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: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris HCl, pH 5.5, 0.2M ammonium acetate, 25 % w/v PEG3350, and 5 mM GMP-PNP., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 7, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→50 Å / Num. all: 76798 / Num. obs: 76184 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.075 / Net I/σ(I): 29.57 |
Reflection shell | Resolution: 2.53→2.57 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.09 / Num. unique all: 3834 / Rsym value: 0.38 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4G63 Resolution: 2.53→44.7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 199674.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.0161 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.53→44.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.53→2.69 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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