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Open data
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Basic information
Entry | Database: PDB / ID: 2hur | ||||||
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Title | Escherichia coli nucleoside diphosphate kinase | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | SIGNALING PROTEIN / TRANSFERASE / TYPE II TETRAMER | ||||||
Function / homology | ![]() purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moynie, L. / Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A. | ||||||
![]() | ![]() Title: The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family Authors: Moynie, L. / Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A. #1: Journal: J.Bacteriol. / Year: 1995 Title: Nucleoside diphosphate kinase from Escherichia coli Authors: Almaula, N. / Lu, Q. / Delgado, J. / Belkin, S. / Inouye, M. #2: ![]() Title: Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 A resolution Authors: Williams, R.L. / Oren, D.A. / Inouye, S. / Inouye, M. / Arnold, E. #3: ![]() Title: Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8 A resolution. Authors: LeBras, G. / Lascu, I. / Lacombe, M.L. / Janin, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.4 KB | Display | ![]() |
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PDB format | ![]() | 146.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.7 KB | Display | ![]() |
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Full document | ![]() | 492.3 KB | Display | |
Data in XML | ![]() | 39.5 KB | Display | |
Data in CIF | ![]() | 56.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nckS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15350.208 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M AMMONIUM SULPHATE, 25% PEG 4000 0.1 M SODIUM ACETATE/ACETIC ACID, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 107 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→38.05 Å / Num. all: 108681 / Num. obs: 108681 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.09 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.38 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB FILE 2NCK Resolution: 1.62→38.05 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2343463.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.0217 Å2 / ksol: 0.368627 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.62→38.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.72 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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