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Yorodumi- PDB-8gqa: Crystal structure of lasso peptide epimerase MslH in complexed wi... -
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-Basic information
Entry | Database: PDB / ID: 8gqa | |||||||||
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Title | Crystal structure of lasso peptide epimerase MslH in complexed with precursor peptide analog MslAdeltaW21 | |||||||||
Components |
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Keywords | ISOMERASE / epimerase / MslH | |||||||||
Function / homology | Bacterial capsule synthesis protein PGA_cap / Capsule synthesis protein, CapA / Bacterial capsule synthesis protein PGA_cap / Metallo-dependent phosphatase-like / metal ion binding / Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein) / : Function and homology information | |||||||||
Biological species | Streptomyces sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | |||||||||
Authors | Nakashima, Y. / Morita, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism. Authors: Nakashima, Y. / Kawakami, A. / Ogasawara, Y. / Maeki, M. / Tokeshi, M. / Dairi, T. / Morita, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gqa.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqa.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 8gqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gqa_validation.pdf.gz | 795.6 KB | Display | wwPDB validaton report |
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Full document | 8gqa_full_validation.pdf.gz | 797.7 KB | Display | |
Data in XML | 8gqa_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 8gqa_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqa ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqa | HTTPS FTP |
-Related structure data
Related structure data | 8gq9SC 8gqbC 8itgC 8ithC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47319.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: WP_063802928.1 / Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: EV578_104528 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V2TW40 |
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#2: Protein/peptide | Mass: 1999.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B2H412 |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-TRS / |
#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: 3.55 Å3/Da / Density % sol: 65.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 5.00 mg/mL MslH, 1.89 mg/mL MslAdeltaW21 with MslB1, 200 mM magnesium chloride, 100 mM Tris-HCl, 28% (w/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.045 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.045 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→45.27 Å / Num. obs: 61142 / % possible obs: 100 % / Redundancy: 27.7 % / Biso Wilson estimate: 43.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.29→2.38 Å / Redundancy: 28.9 % / Rmerge(I) obs: 1.76 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3336 / CC1/2: 0.867 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8GQ9 Resolution: 2.29→45.27 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.3367 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: 47.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→45.27 Å
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Refine LS restraints |
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LS refinement shell |
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