+Open data
-Basic information
Entry | Database: PDB / ID: 1zip | ||||||
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Title | BACILLUS STEAROTHERMOPHILUS ADENYLATE KINASE | ||||||
Components | ADENYLATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / KINASE / ATP-BINDING | ||||||
Function / homology | Function and homology information adenylate kinase / adenylate kinase activity / AMP salvage / phosphorylation / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Berry, M.B. / Phillips Jr., G.N. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. Authors: Berry, M.B. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zip.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zip.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/1zip ftp://data.pdbj.org/pub/pdb/validation_reports/zi/1zip | HTTPS FTP |
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-Related structure data
Related structure data | 1zinC 1zioC 1akyS 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: 24174.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC FINGER / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P27142, adenylate kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-AP5 / |
#5: 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: 1.98 Å3/Da / Density % sol: 43.5 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 / Details: pH 6.9 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown / PH range low: 7.8 / PH range high: 6.8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 2, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→10 Å / Num. obs: 15235 / % possible obs: 97 % / Rmerge(I) obs: 0.096 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AKY Resolution: 1.85→10 Å / Cross valid method: FREE R / σ(F): 0
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Displacement parameters | Biso mean: 13.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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