+Open data
-Basic information
Entry | Database: PDB / ID: 8hlk | ||||||
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Title | Structure of McyB-C1A1 complexed with L-Leu and AMP | ||||||
Components | Microcystin synthetase B (Fragment) | ||||||
Keywords | TOXIN / NRPSs / microcystin synthase / condensation domain / adenylation doamin | ||||||
Function / homology | ADENOSINE MONOPHOSPHATE / LEUCINE Function and homology information | ||||||
Biological species | Microcystis aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Peng, Y.J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of McyB-C1A1 complexed with L-Leu and AMP Authors: Peng, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hlk.cif.gz | 201.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hlk.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 8hlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/8hlk ftp://data.pdbj.org/pub/pdb/validation_reports/hl/8hlk | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 110033.461 Da / Num. of mol.: 1 / Mutation: R464T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microcystis aeruginosa (bacteria) / Gene: mcyB / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-LEU / |
#3: Chemical | ChemComp-AMP / |
#4: 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: 4.15 Å3/Da / Density % sol: 70.35 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 3M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→13.15 Å / Num. obs: 49972 / % possible obs: 99.1 % / Redundancy: 8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.7→2.79 Å / Rmerge(I) obs: 1.274 / Num. unique obs: 4592 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→13.15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.107 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 67.376 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→13.15 Å
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Refine LS restraints |
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