+Open data
-Basic information
Entry | Database: PDB / ID: 3ta1 | ||||||
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Title | A. fulgidus GlnK3, MgADP complex | ||||||
Components | Nitrogen regulatory protein P-II (GlnB-3) | ||||||
Keywords | SIGNALING PROTEIN / PII-family / regulator / Amt3 | ||||||
Function / homology | Function and homology information regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Maier, S. / Schleberger, P. / Lue, W. / Wacker, T. / Pflueger, T. / Litz, C. / Andrade, S.L.A. | ||||||
Citation | Journal: Plos One / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ta1.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ta1.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ta1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/3ta1 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/3ta1 | HTTPS FTP |
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-Related structure data
Related structure data | 3t9zC 3ta0C 3ta2C 3o8wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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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.) Archaeoglobus fulgidus (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: AF_1750, glnK3 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: O28524 #2: Chemical | ChemComp-ADP / #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: 2.3 Å3/Da / Density % sol: 46.49 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Monochromator: Bartels / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→64.02 Å / Num. all: 56191 / Num. obs: 56191 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 39.28 Å2 / Rsym value: 0.048 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.415 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O8W Resolution: 1.9→44.16 Å / Cor.coef. Fo:Fc: 0.9579 / Cor.coef. Fo:Fc free: 0.9494 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.14 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 66.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.329 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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