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Yorodumi- PDB-5gww: Structure of MoeN5-Sso7d fusion protein in complex with a permeth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gww | ||||||
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Title | Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue | ||||||
Components | MoeN5,DNA-binding protein 7d | ||||||
Keywords | TRANSFERASE / DNA BINDING PROTEIN / moenomycin / antibiotics / biosynthesis / prenyl transferase / alpha helical | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces ghanaensis (bacteria) Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ko, T.-P. / Guo, R.-T. / Chen, C.-C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Complex structures of MoeN5 with substrate analogues suggest sequential catalytic mechanism. Authors: Zhang, L. / Ko, T.-P. / Malwal, S.R. / Liu, W. / Zhou, S. / Yu, X. / Oldfield, E. / Guo, R.-T. / Chen, C.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gww.cif.gz | 259.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gww.ent.gz | 206.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gww_validation.pdf.gz | 711.1 KB | Display | wwPDB validaton report |
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Full document | 5gww_full_validation.pdf.gz | 736.4 KB | Display | |
Data in XML | 5gww_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 5gww_validation.cif.gz | 82.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gww ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gww | HTTPS FTP |
-Related structure data
Related structure data | 5gwvC 6j8vC 6j8wC 5b02S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37581.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The fusion protein of MoeN5 (RESIDUES 1-260), LINKER AGAGA (RESIDUES 261-265) and Sso7d (RESIDUES 266-329) Source: (gene. exp.) Streptomyces ghanaensis (bacteria), (gene. exp.) Sulfolobus solfataricus (archaea) Gene: moeN5, sso7d, sso7d-1, SSO10610 / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A010, UniProt: P39476 #2: Chemical | ChemComp-7B5 / | #3: 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: 2.59 Å3/Da / Density % sol: 52.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: protein: 10 mg/mL in 10 mM DTT, 1 mM MgCl2 reservoir: 0.2 M Li3 citrate, 0.3 M NaCl, 25% w/v PEG 3350 cryoprotectant: 5 mM permethylated analogue, 0.3 M Li3 citrate, 0.4 M NaCl, 27% w/v PEG 3350, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 68707 / % possible obs: 98.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.7 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 5B02 Resolution: 2.3→25 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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LS refinement shell | Resolution: 2.3→2.38 Å /
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