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Yorodumi- PDB-6smd: PlMCAT:AntF (holo): type II PKS acyl-carrier protein in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6smd | ||||||
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Title | PlMCAT:AntF (holo): type II PKS acyl-carrier protein in complex with its malonyl-transacylase | ||||||
Components |
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Keywords | PROTEIN BINDING / Natural Product Biosynthesis / Polyketides / Minimal PKS System / Anthraquinone / Chain Elongation / Catalysis | ||||||
Function / homology | Function and homology information [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Photorhabdus luminescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Braeuer, A. / Zhou, Q. / Grammbitter, G.L.C. / Schmalhofer, M. / Ruehl, M. / Kaila, V.R.I. / Bode, H. / Groll, M. | ||||||
Citation | Journal: Nat.Chem. / Year: 2020 Title: Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis. Authors: Brauer, A. / Zhou, Q. / Grammbitter, G.L.C. / Schmalhofer, M. / Ruhl, M. / Kaila, V.R.I. / Bode, H.B. / Groll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6smd.cif.gz | 269.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6smd.ent.gz | 220.1 KB | Display | PDB format |
PDBx/mmJSON format | 6smd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6smd_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 6smd_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 6smd_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 6smd_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/6smd ftp://data.pdbj.org/pub/pdb/validation_reports/sm/6smd | HTTPS FTP |
-Related structure data
Related structure data | 6sm4C 6sm6C 6smoC 6smpC 2g1hS 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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-Components
#1: Protein | Mass: 11191.210 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: C6H68_21855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S8QL96 | ||
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#2: Protein | Mass: 33136.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: fabD, plu2834 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7N385, [acyl-carrier-protein] S-malonyltransferase 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: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.8 M Na/K-phosphate, 4% polypropylene glycol P400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 16593 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.3→3.4 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1402 / CC1/2: 0.917 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G1H Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.863 / SU B: 58.9 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.53 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 191.52 Å2 / Biso mean: 74.66 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 3.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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