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Yorodumi- PDB-1del: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP AND AMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1del | ||||||
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Title | DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP AND AMP | ||||||
Components | DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / TRANSFERASE | ||||||
Function / homology | Function and homology information (deoxy)nucleoside-phosphate kinase / (deoxy)nucleoside-phosphate kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Teplyakov, A. / Sebastiao, P. | ||||||
Citation | Journal: EMBO J. / Year: 1996 Title: Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP. Authors: Teplyakov, A. / Sebastiao, P. / Obmolova, G. / Perrakis, A. / Brush, G.S. / Bessman, M.J. / Wilson, K.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary X-Ray Analysis of Bacteriophage T4 Deoxynucleotide Kinase Authors: Sebastiao, P. / Obmolova, G. / Brush, G.S. / Bessman, M.J. / Teplyakov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1del.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1del.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 1del.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1del ftp://data.pdbj.org/pub/pdb/validation_reports/de/1del | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.98807, -0.13116, 0.08074), Vector: |
-Components
#1: Protein | Mass: 27359.111 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 1 / Plasmid: PBK5 / Gene (production host): 1 / Production host: Escherichia coli (E. coli) References: UniProt: P04531, (deoxy)nucleoside-phosphate kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-AMP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. obs: 31836 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.065 |
Reflection | *PLUS Num. measured all: 96619 |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 39.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 / Rfactor all: 0.186 / Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.027 |