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Open data
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Basic information
Entry | Database: PDB / ID: 3ta0 | ||||||
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Title | A. fulgidus GlnK3, MgATP complex | ||||||
![]() | Nitrogen regulatory protein P-II (GlnB-3) | ||||||
![]() | SIGNALING PROTEIN / PII-family / regulator / Amt3 | ||||||
Function / homology | ![]() regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Maier, S. / Schleberger, P. / Lue, W. / Wacker, T. / Pflueger, T. / Litz, C. / Andrade, S.L.A. | ||||||
![]() | ![]() Title: Mechanism of disruption of the Amt-GlnK complex by P(II)-mediated sensing of 2-oxoglutarate. Authors: Maier, S. / Schleberger, P. / Lu, W. / Wacker, T. / Pfluger, T. / Litz, C. / Andrade, S.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.9 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3t9zC ![]() 3ta1C ![]() 3ta2C ![]() 3o8wS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13164.234 Da / Num. of mol.: 6 / Fragment: UNP residues 12-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: AF_1750, glnK3 / Production host: ![]() ![]() #2: Chemical | ChemComp-ATP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 17% PEG3350, 0.1 M sodium citrate buffer, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Monochromator: VariMax VHF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.44 Å / Num. all: 33011 / Num. obs: 32450 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 56.46 Å2 / Rsym value: 0.092 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.363 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3O8W Resolution: 2.3→29.44 Å / Cor.coef. Fo:Fc: 0.8887 / Cor.coef. Fo:Fc free: 0.8807 / SU R Cruickshank DPI: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.31 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.235 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 62.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.397 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 16
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