+Open data
-Basic information
Entry | Database: PDB / ID: 6wf4 | ||||||
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Title | Crystal Structure of TerC Co-crystallized with Polyporic Acid | ||||||
Components | Terfestatin Biosyntheis Enzyme C | ||||||
Keywords | BIOSYNTHETIC PROTEIN / natural products / jellyroll / Structural Genomics / PSI-Biology / Enzyme Discovery for Natural Product Biosynthesis / NatPro | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / ISOPROPYL ALCOHOL / Chem-U07 / TerC Function and homology information | ||||||
Biological species | Streptomyces sp. RM-5-8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å | ||||||
Authors | Clinger, J.A. / Miller, M.D. / Hall, R.E. / Zhang, Y. / Elshahawi, S.I. / Thorson, J.S. / Van Lanen, S.G. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Structural and functional characterization of two cooperative enzymes responsible for the stability of p-terphenyls. Authors: Clinger, J.A. / Zhang, Y. / Liu, Y. / Miller, M.D. / Hall, R.E. / Van Lanen, S.G. / Phillips Jr., G.N. / Thorson, J.S. / Elshahawri, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wf4.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wf4.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wf4_validation.pdf.gz | 703.1 KB | Display | wwPDB validaton report |
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Full document | 6wf4_full_validation.pdf.gz | 703.6 KB | Display | |
Data in XML | 6wf4_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 6wf4_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/6wf4 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/6wf4 | HTTPS FTP |
-Related structure data
Related structure data | 6d34S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19953.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. RM-5-8 (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3B6UEU1 |
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#2: Chemical | ChemComp-U07 / ( |
#3: Chemical | ChemComp-IPA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.74 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 20% v/v 2-Propanol, 0.1M MES, 20%w/v PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 31, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→48.59 Å / Num. obs: 11538 / % possible obs: 99.2 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.026 / Rrim(I) all: 0.106 / Net I/σ(I): 15.2 / Num. measured all: 171889 / Scaling rejects: 111 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 6D34 Resolution: 1.97→31.81 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.72 Å2 / Biso mean: 50.5429 Å2 / Biso min: 16.98 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→31.81 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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