+Open data
-Basic information
Entry | Database: PDB / ID: 2ar7 | ||||||
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Title | Crystal structure of human adenylate kinase 4, AK4 | ||||||
Components | Adenylate kinase 4 | ||||||
Keywords | TRANSFERASE / AK4 / nucleotide kinase / nucleotide binding / human / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ribonucleoside diphosphate biosynthetic process / nucleoside monophosphate kinase activity / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase activity / nucleoside-diphosphate kinase / nucleobase-containing small molecule interconversion ...ribonucleoside diphosphate biosynthetic process / nucleoside monophosphate kinase activity / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase activity / nucleoside-diphosphate kinase / nucleobase-containing small molecule interconversion / regulation of oxidative phosphorylation / Interconversion of nucleotide di- and triphosphates / GTP metabolic process / nucleoside diphosphate kinase activity / ATP metabolic process / cellular response to hypoxia / mitochondrial matrix / phosphorylation / GTP binding / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Filippakopoulos, P. / Turnbull, A.P. / Fedorov, O. / Weigelt, J. / Bunkoczi, G. / Ugochukwu, E. / Debreczeni, J. / Niesen, F. / von Delft, F. / Edwards, A. ...Filippakopoulos, P. / Turnbull, A.P. / Fedorov, O. / Weigelt, J. / Bunkoczi, G. / Ugochukwu, E. / Debreczeni, J. / Niesen, F. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human adenylate kinase 4, AK4 Authors: Filippakopoulos, P. / Turnbull, A.P. / Fedorov, O. / Weigelt, J. / Bunkoczi, G. / Ugochukwu, E. / Debreczeni, J. / Niesen, F. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ar7.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ar7.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ar7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ar7_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 2ar7_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 2ar7_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 2ar7_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/2ar7 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2ar7 | HTTPS FTP |
-Related structure data
Related structure data | 2bbwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27975.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AK3, AK4 / Plasmid: pLIC-SGC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P27144, adenylate kinase #2: 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: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: sodium succinate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.968 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2005 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→47.95 Å / Num. all: 32401 / Num. obs: 32401 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2704 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2BBW Resolution: 2.15→47.95 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.398 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.179 / 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: 23.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→47.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.205 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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