+Open data
-Basic information
Entry | Database: PDB / ID: 5xz2 | ||||||
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Title | Crystal structure of adenylate kinase | ||||||
Components | Adenylate kinase isoenzyme 1 | ||||||
Keywords | TRANSFERASE / phosphorylation | ||||||
Function / homology | Function and homology information : / AMP metabolic process / purine nucleotide metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process ...: / AMP metabolic process / purine nucleotide metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Moon, S. / Bae, E. / Kim, J. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Structural analyses of adenylate kinases from Antarctic and tropical fishes for understanding cold adaptation of enzymes Authors: Moon, S. / Kim, J. / Bae, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xz2.cif.gz | 162.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xz2.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xz2_validation.pdf.gz | 956.6 KB | Display | wwPDB validaton report |
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Full document | 5xz2_full_validation.pdf.gz | 960.5 KB | Display | |
Data in XML | 5xz2_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 5xz2_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/5xz2 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/5xz2 | HTTPS FTP |
-Related structure data
Related structure data | 5x6kSC 5xruC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
#1: Protein | Mass: 21670.080 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ak1, AK1, zgc:91930 / Production host: Escherichia coli (E. coli) References: UniProt: Q68EH2, adenylate kinase, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | There are remained extra residues (GLY and HIS) after TEV cleavage reaction. | |
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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: 2.39 Å3/Da / Density % sol: 48.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.6, 2.5M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 41960 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 7 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4159 / Rpim(I) all: 0.31 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X6K Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.907 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.117 / 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: 31.269 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→50 Å
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Refine LS restraints |
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