+Open data
-Basic information
Entry | Database: PDB / ID: 6ham | ||||||
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Title | Adenylate kinase | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Adenylat kinase | ||||||
Function / homology | Function and homology information purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / phosphorylation ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å | ||||||
Authors | Kantaev, R. / Inbal, R. / Goldenzweig, A. / Barak, Y. / Dym, O. / Peleg, Y. / Albek, S. / Fleishman, S.J. / Haran, G. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2018 Title: Manipulating the Folding Landscape of a Multidomain Protein. Authors: Kantaev, R. / Riven, I. / Goldenzweig, A. / Barak, Y. / Dym, O. / Peleg, Y. / Albeck, S. / Fleishman, S.J. / Haran, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ham.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ham.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ham.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6ham ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6ham | HTTPS FTP |
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-Related 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: 23696.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase |
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#2: Chemical | ChemComp-AP5 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.14 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 14% PEG 4000 0.05M Tris pH=8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→46.73 Å / Num. obs: 8598 / % possible obs: 99.98 % / Redundancy: 2.6 % / Rsym value: 0.02 / Net I/σ(I): 23.43 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 2.1 % / Num. unique obs: 864 / Rsym value: 0.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.55→58.44 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.072 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.594 / ESU R Free: 0.289 / 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: 58.487 Å2
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Refinement step | Cycle: 1 / Resolution: 2.55→58.44 Å
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Refine LS restraints |
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