+Open data
-Basic information
Entry | Database: PDB / ID: 7de3 | ||||||
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Title | Human adenylate kinase 1 (hAK1) mutant-R128W | ||||||
Components | Adenylate kinase isoenzyme 1 | ||||||
Keywords | TRANSFERASE / cellular energy homeostasis / adenine nucleotide metabolism / CELL CYCLE | ||||||
Function / homology | Function and homology information nucleoside-triphosphate-adenylate kinase / outer dense fiber / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / (d)CMP kinase activity / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase ...nucleoside-triphosphate-adenylate kinase / outer dense fiber / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / (d)CMP kinase activity / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / phosphorylation / extracellular exosome / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å | ||||||
Authors | Lin, W. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of human adenylate kinase 1 mutant-R128W. Authors: Lin, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7de3.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7de3.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 7de3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7de3_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 7de3_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 7de3_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 7de3_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7de3 ftp://data.pdbj.org/pub/pdb/validation_reports/de/7de3 | HTTPS FTP |
-Related structure data
Related structure data | 3adkS 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: 21696.891 Da / Num. of mol.: 1 / Mutation: R128W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AK1 / Production host: Escherichia coli (E. coli) References: UniProt: P00568, adenylate kinase, nucleoside-diphosphate kinase |
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#2: 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: 50.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350,0.2M Ammonium acetate / PH range: 6.6-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.197→33.647 Å / Num. obs: 11451 / % possible obs: 97.69 % / Redundancy: 13.5 % / CC1/2: 0.938 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.197→2.275 Å / Rmerge(I) obs: 0.154 / Num. unique obs: 22139 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3adk Resolution: 2.197→33.647 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 89.08 Å2 / Biso mean: 32.0887 Å2 / Biso min: 9.39 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.197→33.647 Å
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