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Yorodumi- PDB-3quo: Crystal structure of fosfomycin resistance kinase FomA from Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3quo | ||||||
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Title | Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with ATP and fosfomycin | ||||||
Components | FomA protein | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / fosfomycin / antibiotic resistance / phosphoryl transfer / kinase / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
Function / homology | Function and homology information 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 | Streptomyces wedmorensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Pakhomova, S. / Bartlett, S.G. / Doerner, P.A. / Newcomer, M.E. | ||||||
Citation | Journal: Biochemistry / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3quo.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3quo.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 3quo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3quo_validation.pdf.gz | 774.4 KB | Display | wwPDB validaton report |
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Full document | 3quo_full_validation.pdf.gz | 778.9 KB | Display | |
Data in XML | 3quo_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3quo_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/3quo ftp://data.pdbj.org/pub/pdb/validation_reports/qu/3quo | HTTPS FTP |
-Related structure data
Related structure data | 3qunC 3qurC 3qvfC 3qvhC 3d40S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Streptomyces wedmorensis (bacteria) / Gene: fomA, fosfomycin resistance kinase / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56187 |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-FCN / |
#4: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 17 % PEG3350, 25 % glycerol, 0.1 M MES, 10 mM ATP, 10 mM fosfomycin , pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 10, 2008 / 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: 1.58→50 Å / Num. all: 42575 / Num. obs: 42575 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.039 / Net I/σ(I): 35.6 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4204 / Rsym value: 0.561 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3D40 Resolution: 1.58→26.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.778 / SU ML: 0.045 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / 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: 31.701 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→26.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.621 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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