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Yorodumi- PDB-8osz: Structural and functional studies of geldanamycin amide synthase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8osz | ||||||
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Title | Structural and functional studies of geldanamycin amide synthase ShGdmF | ||||||
Components | GdmF | ||||||
Keywords | BIOSYNTHETIC PROTEIN / amide synthase / geldanamycin / amidase / alpha-beta | ||||||
Function / homology | : / Arylamine N-acetyltransferase / N-acetyltransferase / arylamine N-acetyltransferase activity / Papain-like cysteine peptidase superfamily / ACETATE ION / 3-aminophenol / DI(HYDROXYETHYL)ETHER / GdmF Function and homology information | ||||||
Biological species | Streptomyces hygroscopicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Ewert, W. / Zeilinger, C. / Kirschning, A. / Preller, M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structural and functional studies of geldanamycin amide synthase ShGdmF Authors: Ewert, W. / Bartens, C. / Heutling, A. / Ongouta, J. / Vogt, M. / Kishore, A. / Zeilinger, C. / Preller, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8osz.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8osz.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 8osz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8osz_validation.pdf.gz | 809.7 KB | Display | wwPDB validaton report |
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Full document | 8osz_full_validation.pdf.gz | 810.5 KB | Display | |
Data in XML | 8osz_validation.xml.gz | 13 KB | Display | |
Data in CIF | 8osz_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/8osz ftp://data.pdbj.org/pub/pdb/validation_reports/os/8osz | HTTPS FTP |
-Related structure data
Related structure data | 8btmC 8oomC 8osvC 8ot2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 29889.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: gdmF / Production host: Escherichia coli (E. coli) / References: UniProt: Q84G21 |
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#2: Chemical | ChemComp-K5V / |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-ACT / |
#5: 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: 2.59 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 25 % PEG4000, 150 mM sodium acetate, 200 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→43.24 Å / Num. obs: 82845 / % possible obs: 99.92 % / Redundancy: 13.3 % / Biso Wilson estimate: 16.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04587 / Net I/σ(I): 24.42 |
Reflection shell | Resolution: 1.26→1.305 Å / Rmerge(I) obs: 0.9903 / Num. unique obs: 8191 / CC1/2: 0.878 / Rrim(I) all: 2.08 / % possible all: 99.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→43.24 Å / SU ML: 0.1131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7699 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 23.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→43.24 Å
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Refine LS restraints |
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LS refinement shell |
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