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Open data
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Basic information
| Entry | Database: PDB / ID: 2bwj | ||||||
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| Title | Structure of adenylate kinase 5 | ||||||
Components | ADENYLATE KINASE 5 | ||||||
Keywords | TRANSFERASE / ADENYLATE KINASE / PHOSPHORYL TRANSFER REACTION | ||||||
| Function / homology | Function and homology informationdADP biosynthetic process / ADP biosynthetic process / adenylate kinase / pyrimidine ribonucleotide biosynthetic process / AMP kinase activity / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / centriolar satellite ...dADP biosynthetic process / ADP biosynthetic process / adenylate kinase / pyrimidine ribonucleotide biosynthetic process / AMP kinase activity / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / centriolar satellite / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
| Biological species | HOMO SAPIENS (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Bunkoczi, G. / Filippakopoulos, P. / Fedorov, O. / Jansson, A. / Longman, E. / Ugochukwu, E. / Knapp, S. / von Delft, F. / Arrowsmith, C. / Edwards, A. ...Bunkoczi, G. / Filippakopoulos, P. / Fedorov, O. / Jansson, A. / Longman, E. / Ugochukwu, E. / Knapp, S. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. | ||||||
Citation | Journal: To be PublishedTitle: Structure of Adenylate Kinase 5 Authors: Filippakopoulos, P. / Bunkoczi, G. / Jansson, A. / Longman, E. / Knapp, S. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2bwj.cif.gz | 241.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2bwj.ent.gz | 195.2 KB | Display | PDB format |
| PDBx/mmJSON format | 2bwj.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/2bwj ftp://data.pdbj.org/pub/pdb/validation_reports/bw/2bwj | HTTPS FTP |
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-Related structure data
| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 3 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
| #1: Protein | Mass: 22176.564 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 135 TO MET ENGINEERED RESIDUE IN CHAIN B, ARG 135 TO MET ...ENGINEERED | Sequence details | RESIDUE 1 REMAINS FROM HIS-TAG AFTER TEV CLEAVAGE | |
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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: 4.2 Å3/Da / Density % sol: 70.7 % / Description: NCS AVERAGING DONE WITH DM. |
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| Crystal grow | pH: 7.5 Details: 0.1M HEPES PH7.5, 0.1M NACL, 1.6M (NH4)2SO4, pH 7.50 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9184 |
| Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 13, 2005 / Details: MIRRORS |
| Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
| Reflection | Resolution: 2.3→48.15 Å / Num. obs: 7913 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.53 |
| Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.35 / % possible all: 63.1 |
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Processing
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| Refinement | Method to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 9.839 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.172 / 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: 56.12 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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| Refine LS restraints |
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About Yorodumi




HOMO SAPIENS (human)
X-RAY DIFFRACTION
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