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Yorodumi- PDB-5b03: Structure of MoeN5-Sso7d fusion protein in complex with geranyl p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b03 | ||||||
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Title | Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate | ||||||
Components | MoeN5,DNA-binding protein 7d | ||||||
Keywords | TRANSFERASE / DNA BINDING PROTEIN / prenyltransferase / alpha-helical fold / ligand complex / fusion tag | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces ghanaensis (bacteria) Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ko, T.-P. / Zhang, L. / Chen, C.-C. / Guo, R.-T. / Oldfield, E.O. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Moenomycin Biosynthesis: Structure and Mechanism of Action of the Prenyltransferase MoeN5. Authors: Zhang, L. / Chen, C.C. / Ko, T.P. / Huang, J.W. / Zheng, Y. / Liu, W. / Wang, I. / Malwal, S.R. / Feng, X. / Wang, K. / Huang, C.H. / Hsu, S.T. / Wang, A.H. / Oldfield, E. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b03.cif.gz | 250.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b03.ent.gz | 200.9 KB | Display | PDB format |
PDBx/mmJSON format | 5b03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/5b03 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/5b03 | HTTPS FTP |
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-Related structure data
Related structure data | 5b00C 5b02SC 5b0iC 5b0jC 5b0kC 5b0lC 5b0mC 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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2 |
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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 prenyltransferase (RESIDUES 1-260), LINKER AGAGA (RESIDUES 261-265) and Sso7d (RESIDUES 266-329) Source: (gene. exp.) Streptomyces ghanaensis (bacteria), (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (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-GPP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: 0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5mM GPP, 0.3M Li3-citrate, 0.4M NaCl, 27% PEG 3350, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. obs: 47970 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B02 Resolution: 2.6→25 Å / Cross valid method: THROUGHOUT
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Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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