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- PDB-3qun: Crystal structure of fosfomycin resistance kinase FomA from Strep... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qun | ||||||
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Title | Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgATP | ||||||
![]() | FomA protein | ||||||
![]() | TRANSFERASE / fosfomycin / antibiotic resistance / phosphoryl transfer / kinase | ||||||
Function / homology | ![]() isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / glutamate 5-kinase activity / proline biosynthetic process / isoprenoid biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pakhomova, S. / Bartlett, S.G. / Doerner, P.A. / Newcomer, M.E. | ||||||
![]() | ![]() Title: Structural and biochemical insights into the mechanism of fosfomycin phosphorylation by fosfomycin resistance kinase FomA. Authors: Pakhomova, S. / Bartlett, S.G. / Doerner, P.A. / Newcomer, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.2 KB | Display | ![]() |
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PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.9 KB | Display | ![]() |
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Full document | ![]() | 787.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3quoC ![]() 3qurC ![]() 3qvfC ![]() 3qvhC ![]() 3d40S 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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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two-fold axis: y,x,-z |
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Components
#1: Protein | Mass: 30876.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS STATE THAT THE DEPOSITED SEQUENCE UNPROT ENTRY Q56187 IS WRONG AT POSITION 31 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% PEG3350, 15% glycerol, 0.1M MES, 10mM ATP, 10 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38079 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→40 Å / Num. all: 26774 / Num. obs: 26774 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 33.2 Å2 / Rsym value: 0.036 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2724 / Rsym value: 0.454 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3D40 Resolution: 1.87→23.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.518 / SU ML: 0.082 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R Free: 0.115 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.874 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→23.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.918 Å / Total num. of bins used: 20
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