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Yorodumi- PDB-2rgx: Crystal Structure of Adenylate Kinase from Aquifex Aeolicus in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rgx | ||||||
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Title | Crystal Structure of Adenylate Kinase from Aquifex Aeolicus in complex with Ap5A | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Transferase(Phosphotransferase) / ATP-binding / Kinase / Nucleotide-binding | ||||||
Function / homology | Function and homology information nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / phosphorylation / intracellular membrane-bounded organelle / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Thai, V. / Wolf-Watz, M. / Fenn, T. / Pozharski, E. / Wilson, M.A. / Petsko, G.A. / Kern, D. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Intrinsic motions along an enzymatic reaction trajectory. Authors: Henzler-Wildman, K.A. / Thai, V. / Lei, M. / Ott, M. / Wolf-Watz, M. / Fenn, T. / Pozharski, E. / Wilson, M.A. / Petsko, G.A. / Karplus, M. / Hubner, C.G. / Kern, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rgx.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rgx.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 2rgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/2rgx ftp://data.pdbj.org/pub/pdb/validation_reports/rg/2rgx | HTTPS FTP |
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-Related structure data
Related structure data | 2rh5C 1akeS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23269.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: adk / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: O66490, adenylate kinase | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-AP5 / | #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: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 25%(v/v) PEG MME 550, 0.1 M MES pH 6.5, 0.01 M Zinc Sulfate, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2004 |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 18796 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.092 / Χ2: 1 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.546 / Num. unique all: 1819 / Χ2: 0.904 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AKE Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.632 / SU ML: 0.108 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.967 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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