+Open data
-Basic information
Entry | Database: PDB / ID: 4gf5 | ||||||
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Title | Crystal Structure of Calicheamicin Methyltransferase, CalS11 | ||||||
Components | CalS11 | ||||||
Keywords | TRANSFERASE / CalS11 / SAH / Methyltransferase / Calicheamicin / Structural Genomics / Protein Structure Initiative / PSI / PSI-Biology / NATPRO / Enzyme Discovery for Natural Products Biosynthesis / Center for Eukaryotic Structural Genomics / CESG / Enzyme Discovery for Natural Product Biosynthesis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Micromonospora echinospora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Helmich, K.E. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: to be published | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gf5.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4gf5.ent.gz | 860.1 KB | Display | PDB format |
PDBx/mmJSON format | 4gf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gf5_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 4gf5_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 4gf5_validation.xml.gz | 195.5 KB | Display | |
Data in CIF | 4gf5_validation.cif.gz | 268.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/4gf5 ftp://data.pdbj.org/pub/pdb/validation_reports/gf/4gf5 | HTTPS FTP |
-Related structure data
Related structure data | 3tosS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological unit is a decamer. There are 2 biological units in the asymmetric unit (chains A-J and chains K-T) |
-Components
#1: Protein | Mass: 28950.844 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: Micromonospora echinospora / Gene: AAM70337, calS11 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8KNF1 #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Protein solution (11 mg/ml CalS11, 25mM Tris pH 8.0, 5 mg/ml calicheamicin) mixed in a 1:1 ratio with the well solution (25% PEG 3350, .2M LiSO4, .1M Tris pH 8.5) Cryoprotected with 30% PEG ...Details: Protein solution (11 mg/ml CalS11, 25mM Tris pH 8.0, 5 mg/ml calicheamicin) mixed in a 1:1 ratio with the well solution (25% PEG 3350, .2M LiSO4, .1M Tris pH 8.5) Cryoprotected with 30% PEG 3350, .2M LiSO4, .1M Tris pH 8.5, Vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. all: 254196 / Num. obs: 254196 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Χ2: 0.797 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3TOS Resolution: 2.2→49.322 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8689 / SU ML: 0.25 / σ(F): 0 / Phase error: 20.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.75 Å2 / Biso mean: 15.2599 Å2 / Biso min: 1.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.322 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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