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Yorodumi- PDB-3d41: Crystal structure of fosfomycin resistance kinase FomA from Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d41 | ||||||
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Title | Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgAMPPNP and fosfomycin | ||||||
Components | FomA protein | ||||||
Keywords | TRANSFERASE / fosfomycin / antibiotic resistance / kinase / phosphoryl transfer | ||||||
Function / homology | Function and homology information isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Streptomyces wedmorensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pakhomova, S. / Bartlett, S.G. / Augustus, A. / Kuzuyama, T. / Newcomer, M.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis. Authors: Pakhomova, S. / Bartlett, S.G. / Augustus, A. / Kuzuyama, T. / 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 | 3d41.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d41.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/3d41 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/3d41 | HTTPS FTP |
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-Related structure data
Related structure data | 3d40SC 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 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56187 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-FCN / |
#5: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT THE RESEQUENCI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 11% PEG 3350, 0.1 M tri-ammonium citrate, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38074 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38074 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 17293 / Num. obs: 17293 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 46.3 Å2 / Rsym value: 0.071 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1664 / Rsym value: 0.557 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3D40 Resolution: 2.2→29.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.56 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.213 / 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: 43.194 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.04 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.2 Å / Num. reflection Rwork: 920 / Total num. of bins used: 20 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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