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Yorodumi- PDB-8gic: A1 Tei + Hpg: Adenylation domain 1 core construct from teicoplani... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gic | |||||||||
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Title | A1 Tei + Hpg: Adenylation domain 1 core construct from teicoplanin biosynthesis; 4-hydroxyphenylglycine bound | |||||||||
Components |
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Keywords | LIGASE / AMP-binding enzyme / NRPS / Adenylation domain | |||||||||
Function / homology | Function and homology information lipid biosynthetic process / phosphopantetheine binding / catalytic activity Similarity search - Function | |||||||||
Biological species | Actinoplanes teichomyceticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Hansen, M.H. / Cryle, M.J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides. Authors: Hansen, M.H. / Adamek, M. / Iftime, D. / Petras, D. / Schuseil, F. / Grond, S. / Stegmann, E. / Cryle, M.J. / Ziemert, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gic.cif.gz | 433.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gic.ent.gz | 288.1 KB | Display | PDB format |
PDBx/mmJSON format | 8gic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/8gic ftp://data.pdbj.org/pub/pdb/validation_reports/gi/8gic | HTTPS FTP |
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-Related structure data
Related structure data | 8gj4C 8gjpC 8gkmC 8glcC 1amuS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42084.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria) Gene: tcp9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AZ9 #2: Protein | Mass: 7636.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria) Gene: tcp13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AZ5 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.32 Å3/Da / Density % sol: 46.99 % / Description: Cuboid |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MMT (L-Malic acid, MES and Tris in a ratio of 1:2:2), pH 6 and 25% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→44.15 Å / Num. obs: 114836 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 21.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02163 / Rpim(I) all: 0.02163 / Net I/σ(I): 14.32 |
Reflection shell | Resolution: 1.64→1.699 Å / Rmerge(I) obs: 0.3679 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 11325 / CC1/2: 0.767 / Rpim(I) all: 0.3679 / % possible all: 99.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AMU Resolution: 1.64→44.15 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7051 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→44.15 Å
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Refine LS restraints |
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LS refinement shell |
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