+Open data
-Basic information
Entry | Database: PDB / ID: 2eg2 | ||||||
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Title | The crystal structure of PII protein | ||||||
Components | Nitrogen regulatory protein P-II | ||||||
Keywords | SIGNALING PROTEIN / Nitrogen regulatory protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Sakai, H. / Shinkai, A. / Kitamura, Y. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: The crystal structure of PII protein Authors: Sakai, H. / Shinkai, A. / Kitamura, Y. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eg2.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eg2.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 2eg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/2eg2 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/2eg2 | HTTPS FTP |
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-Related structure data
Related structure data | 2eg1SC 2z0gC 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12515.567 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: glnB / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O66513 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-ATP / |
#4: 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: 1.83 Å3/Da / Density % sol: 32.88 % |
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Crystal grow | Temperature: 291 K / pH: 4.6 Details: ammonium acetate, sodium acetate trihydrate, PEG4000, glycerol anhydrous, pH4.6, microbatch method, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 13, 2006 / Details: DIAMOND TRICHROMATOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→100 Å / Num. obs: 9892 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 8.77 / Num. unique all: 976 / Rsym value: 0.292 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EG1 Resolution: 1.72→33.46 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 312811.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.8403 Å2 / ksol: 0.366167 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.72→33.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.83 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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