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Yorodumi- PDB-1dvr: STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dvr | ||||||
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Title | STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP | ||||||
Components | ADENYLATE KINASE | ||||||
Keywords | TRANSFERASE (PHOSPHOTRANSFERASE) / NUCLEOSIDE MONOPHOSPHATE KINASE / MYOKINASE | ||||||
Function / homology | Function and homology information pre-replicative complex assembly / AMP metabolic process / ADP biosynthetic process / Interconversion of nucleotide di- and triphosphates / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication origin binding / DNA replication initiation / ATP metabolic process ...pre-replicative complex assembly / AMP metabolic process / ADP biosynthetic process / Interconversion of nucleotide di- and triphosphates / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication origin binding / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / mitochondrion / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.36 Å | ||||||
Authors | Schlauderer, G.J. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. Authors: Schlauderer, G.J. / Proba, K. / Schulz, G.E. #1: Journal: Eur.J.Biochem. / Year: 1995 Title: Stability, Activity and Structure of Adenylate Kinase Mutants Authors: Spuergin, P. / Abele, U. / Schulz, G.E. #2: Journal: Protein Sci. / Year: 1995 Title: High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer Authors: Abele, U. / Schulz, G.E. #3: Journal: Structure / Year: 1995 Title: Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases Authors: Vonrhein, C. / Schlauderer, G.J. / Schulz, G.E. #4: Journal: Nucleic Acids Res. / Year: 1987 Title: The C-DNA Sequence Encoding Cytosolic Adenylate Kinase from Baker'S Yeast (Saccharomyces Cerevisiae) Authors: Proba, K. / Tomasselli, A.G. / Nielsen, P. / Schulz, G.E. #5: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of the Complex of Yeast Adenylate Kinase with the Inhibitor Ap5A at 2.6 Angstroms Resolution Authors: Egner, U. / Tomasselli, A.G. / Schulz, G.E. #6: Journal: Eur.J.Biochem. / Year: 1986 Title: The Complete Amino Acid Sequence of Adenylate Kinase from Baker'S Yeast Authors: Tomasselli, A.G. / Mast, E. / Janes, W. / Schiltz, E. | ||||||
History |
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Remark 700 | SHEET THE HELIX AND SHEET ASSIGNMENTS BELOW ARE AUTOMATIC WITH PROGRAM DSSP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dvr.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dvr.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dvr_validation.pdf.gz | 994.6 KB | Display | wwPDB validaton report |
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Full document | 1dvr_full_validation.pdf.gz | 1005 KB | Display | |
Data in XML | 1dvr_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1dvr_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dvr ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dvr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 92 / 2: CIS PROLINE - PRO B 92 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.489945, -0.809503, -0.323511), Vector: |
-Components
#1: Protein | Mass: 24008.525 Da / Num. of mol.: 2 / Mutation: D89V, R165I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cellular location: CYTOSOL / Plasmid: PUAKYI / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P07170, adenylate kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: 1991 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→10 Å / Num. obs: 15793 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.058 |
Reflection | *PLUS Rmerge(I) obs: 0.058 |
-Processing
Software |
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Refinement | Resolution: 2.36→10 Å / σ(F): 0 Details: RESIDUES SER 166 - ASN 169 IN CHAIN HAVE WEAK DENSITY.
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |