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- PDB-2anb: Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2anb | ||||||
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Title | Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GMP | ||||||
![]() | Guanylate kinase | ||||||
![]() | TRANSFERASE / GMP kinase / guanylate kinase / oligomeric | ||||||
Function / homology | ![]() guanylate kinase / guanylate kinase activity / phosphorylation / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hible, G. / Renault, L. / Schaeffer, F. / Christova, P. / Radulescu, A.Z. / Evrin, C. / Gilles, A.M. / Cherfils, J. | ||||||
![]() | ![]() Title: Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase Authors: Hible, G. / Renault, L. / Schaeffer, F. / Christova, P. / Radulescu, A.Z. / Evrin, C. / 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 | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 40.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.6 KB | Display | ![]() |
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Full document | ![]() | 780.5 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2an9SC ![]() 2ancC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF A MONOMER. The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the 5 operations: 1:matrix= ( -0.50000 -0.86603 0.00000 ) ( 0.86603 -0.50000 0.00000 ) ( 0.00000 0.00000 1.00000 ) translation= ( 106.72798 -0.00010 0.00001 ) 2: matrix= ( -0.50000 0.86603 0.00000 ) ( -0.86603 -0.50000 0.00000 ) ( 0.00000 0.00000 1.00000 ) translation= ( 53.36393 92.42904 -0.00008 ) 3:matrix= ( -0.50000 0.86602 0.00000 ) ( 0.86602 0.50000 0.00000 ) ( 0.00000 0.00000 -1.00000 ) translation= ( 53.36408 -30.80985 103.51692 ) 4:matrix= ( -0.50000 -0.86603 0.00000 ) ( -0.86603 0.50000 0.00000 ) ( 0.00000 0.00000 -1.00000 ) translation= ( 106.72797 61.61937 103.51704 ) 5:matrix= ( 1.00000 0.00000 0.00000 ) ( 0.00000 -1.00000 0.00000 ) ( 0.00000 0.00000 -1.00000 ) translation= ( 0.00000 61.61900 103.51700 ) |
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Components
#1: Protein | Mass: 23625.725 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-5GP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 65.8 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.4M ammonium sulfate, 0.2M lithium chloride, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19 Å / Num. all: 7689 / Num. obs: 7689 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 67.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 5.8 / Num. unique all: 553 / % possible all: 99.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AN9 Resolution: 2.9→19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.365 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.004 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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