+Open data
-Basic information
Entry | Database: PDB / ID: 4mkg | ||||||
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Title | Crystal structure of a stable adenylate kinase variant AKv8 | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Adenylate kinase / Zinc Finger / transferase activity / phosphotransferase activity / Zinc binding / ATP binding / Phosphorylation | ||||||
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 / zinc ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Moon, S. / Jung, D. / Bae, E. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: An integrated approach for thermal stabilization of a mesophilic adenylate kinase. Authors: Moon, S. / Jung, D.K. / Phillips Jr., G.N. / Bae, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mkg.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mkg.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/4mkg ftp://data.pdbj.org/pub/pdb/validation_reports/mk/4mkg | HTTPS FTP |
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-Related structure data
Related structure data | 4mkfC 4mkhC 1p3jS 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
#1: Protein | Mass: 24146.609 Da / Num. of mol.: 1 Mutation: L3I,G17A,D23K,K69R,G73S,D75S,Y103M,K105R,E114Q,D118E,V119E,S169T,Q180A,D184A,S187D,E188S,G190E,Y191V,A193V,Y205F,D210V,L211I,K217Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: adk, BSU01370 / Production host: Escherichia coli (E. coli) / References: UniProt: P16304, adenylate kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-AP5 / |
#5: 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: 2.49 Å3/Da / Density % sol: 50.65 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.4M trisodium citrate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2010 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→44.62 Å / Num. all: 43604 / Num. obs: 43604 / % possible obs: 100 % |
Reflection shell | Resolution: 1.45→1.53 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P3J Resolution: 1.45→36.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.186 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.775 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→36.08 Å
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Refine LS restraints |
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