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- PDB-2f3r: Crystal Structure Of E.coli Guanylate Kinase In Complex With Ap5G -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f3r | ||||||
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Title | Crystal Structure Of E.coli Guanylate Kinase In Complex With Ap5G | ||||||
![]() | Guanylate kinase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hible, G. / Cherfils, J. | ||||||
![]() | ![]() Title: Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G. Authors: Hible, G. / Daalova, P. / Gilles, A.M. / Cherfils, 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 | ![]() | 95.2 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2f3tC ![]() 2an9S C: citing same article ( 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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1 | ![]()
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Unit cell |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF A DIMER (CHAINS A and B). The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z. |
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Components
#1: Protein | ![]() Mass: 23625.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 4000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→28 Å / Num. all: 13344 / Num. obs: 13344 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 7 / Num. unique all: 2192 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2AN9 Resolution: 2.5→27.96 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1728695.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.4334 Å2 / ksol: 0.312595 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→27.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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