+Open data
-Basic information
Entry | Database: PDB / ID: 5wpr | ||||||||||||||||||
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Title | Crystal structure HpiC1 in C2 space group | ||||||||||||||||||
Components | 12-epi-hapalindole C/U synthase | ||||||||||||||||||
Keywords | ISOMERASE / cyclase | ||||||||||||||||||
Function / homology | 12-epi-hapalindole C/U synthase Function and homology information | ||||||||||||||||||
Biological species | Fischerella sp. ATCC 43239 (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||||||||||||||
Authors | Newmister, S.A. / Li, S. / Garcia-Borras, M. / Sanders, J.N. / Yang, S. / Lowell, A.N. / Yu, F. / Smith, J.L. / Williams, R.M. / Houk, K.N. / Sherman, D.H. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis. Authors: Newmister, S.A. / Li, S. / Garcia-Borras, M. / Sanders, J.N. / Yang, S. / Lowell, A.N. / Yu, F. / Smith, J.L. / Williams, R.M. / Houk, K.N. / Sherman, D.H. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wpr.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wpr.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 5wpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/5wpr ftp://data.pdbj.org/pub/pdb/validation_reports/wp/5wpr | HTTPS FTP |
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-Related structure data
Related structure data | 5wppSC 5wpsC 5wpuC 6al6C 6al7C 6al8C 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: 24525.115 Da / Num. of mol.: 1 / Fragment: residues 26-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fischerella sp. ATCC 43239 (bacteria) / Gene: hpiU5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076NBW8 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 22% PEG 4000, 150 mM CaCl2, 100 mM Tris pH 8.5, 5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2017 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→45.11 Å / Num. obs: 45278 / % possible obs: 99.7 % / Redundancy: 6.6 % / Net I/σ(I): 19.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WPP Resolution: 1.49→45.108 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.87 Å2 / Biso mean: 25.6858 Å2 / Biso min: 13.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→45.108 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Origin x: 12.717 Å / Origin y: -24.4043 Å / Origin z: -7.0224 Å
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Refinement TLS group |
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