+Open data
-Basic information
Entry | Database: PDB / ID: 4xc9 | ||||||
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Title | Crystal Structure of apo HygX from Streptomyces hygroscopicus | ||||||
Components | oxidase/hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / double stranded beta helix | ||||||
Function / homology | q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / oxidoreductase activity / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Putative oxidase/hydroxylase Function and homology information | ||||||
Biological species | Streptomyces hygroscopicus subsp. hygroscopicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | McCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily. Authors: McCulloch, K.M. / McCranie, E.K. / Smith, J.A. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xc9.cif.gz | 305 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xc9.ent.gz | 248 KB | Display | PDB format |
PDBx/mmJSON format | 4xc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xc9_validation.pdf.gz | 480.2 KB | Display | wwPDB validaton report |
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Full document | 4xc9_full_validation.pdf.gz | 492 KB | Display | |
Data in XML | 4xc9_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 4xc9_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xc9 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xc9 | HTTPS FTP |
-Related structure data
Related structure data | 4xaaC 4xabC 4xacC 4xbzC 4xcaSC 4xcbC 4zpiC 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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2 |
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Unit cell |
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Details | The biological assembly is a tetramer. The asymmetric unit contains one complete biological unit (chains A, B, C, & D) and half of a second biological unit (chains E & F). The second tetramer is generated by the operation: -x, -y, z |
-Components
#1: Protein | Mass: 28981.477 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus subsp. hygroscopicus (bacteria) Gene: hygX / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2MFS1 #2: Chemical | ChemComp-TRS / #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: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 100 mM Bis-Tris, 100 mM MgCl2, 12% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 61662 / % possible obs: 92.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 38.69 Å2 / Rmerge(I) obs: 0.08 / Χ2: 0.965 / Net I/av σ(I): 14.736 / Net I/σ(I): 9.7 / Num. measured all: 228727 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4XCA Resolution: 2.4→49.295 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.85 / 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: 94.51 Å2 / Biso mean: 40.6367 Å2 / Biso min: 18.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→49.295 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: 22
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