+Open data
-Basic information
Entry | Database: PDB / ID: 6x7p | ||||||
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Title | LnmK in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA | ||||||
Components | Conserved hypthetical protein | ||||||
Keywords | transferase/transferase inhibitor / transferase / lyase / inhibitor / isostere / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces atroolivaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Stunkard, L.M. / Kick, B.J. / Lohman, J.R. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Structures of LnmK, a Bifunctional Acyltransferase/Decarboxylase, with Substrate Analogues Reveal the Basis for Selectivity and Stereospecificity. Authors: Stunkard, L.M. / Kick, B.J. / Lohman, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x7p.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x7p.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 6x7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/6x7p ftp://data.pdbj.org/pub/pdb/validation_reports/x7/6x7p | HTTPS FTP |
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-Related structure data
Related structure data | 6x7lC 6x7mC 6x7nC 6x7oC 4hzoS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35380.387 Da / Num. of mol.: 1 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces atroolivaceus (bacteria) / Gene: LnmK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GGP1 | ||||
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#2: Chemical | ChemComp-SO5 / ( | ||||
#3: Chemical | ChemComp-LCV / ( | ||||
#4: Chemical | ChemComp-SO4 / #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: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 9% PEG400, 100 mM Bis-Tris pH 7.5, 28% PEG3350 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2016 / Details: MD2 microdifractometer |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 51370 / % possible obs: 99.1 % / Redundancy: 17.9 % / Biso Wilson estimate: 32.29 Å2 / Rmerge(I) obs: 0.261 / Rsym value: 0.288 / Net I/σ(I): 91.9 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4621 / Rsym value: 1 / % possible all: 91.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HZO Resolution: 1.55→47.23 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.787 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→47.23 Å
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Refine LS restraints |
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