+Open data
-Basic information
Entry | Database: PDB / ID: 6hap | ||||||
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Title | Adenylate kinase | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Adenylat kinase | ||||||
Function / homology | Function and homology information adenylate kinase / adenylate kinase activity / AMP salvage / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O139:H28 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 6hap.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hap.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6hap ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6hap | HTTPS FTP |
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-Related structure data
Related structure data | 6hamC 4jzkS 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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Unit cell |
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-Components
#1: Protein | Mass: 23696.107 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria) Strain: E24377A / ETEC / Gene: adk, EcE24377A_0513 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: A7ZIN4, 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: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 10% PEG 3350 0.05M Tris pH=5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5417 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→43.49 Å / Num. obs: 7058 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rsym value: 0.0356 / Net I/σ(I): 16.48 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.8 % / Num. unique obs: 696 / Rsym value: 0.3 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JZK Resolution: 2.7→43.49 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→43.49 Å
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Refine LS restraints |
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LS refinement shell |
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