+Open data
-Basic information
Entry | Database: PDB / ID: 8gqb | |||||||||
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Title | Crystal structure of lasso peptide epimerase MslH D11A mutant | |||||||||
Components | Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein) | |||||||||
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 / DI(HYDROXYETHYL)ETHER / 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: 2.41 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 | 8gqb.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqb.ent.gz | 144.8 KB | Display | PDB format |
PDBx/mmJSON format | 8gqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gqb_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
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Full document | 8gqb_full_validation.pdf.gz | 812.1 KB | Display | |
Data in XML | 8gqb_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 8gqb_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqb ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqb | HTTPS FTP |
-Related structure data
Related structure data | 8gq9SC 8gqaC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47275.391 Da / Num. of mol.: 1 / Mutation: D11A 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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-Non-polymers , 5 types, 131 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-TRS / |
#6: Water | ChemComp-HOH / |
-Details
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: 3.65 Å3/Da / Density % sol: 66.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 5.00 mg/mL MslH D11A, 200 mM magnesium chloride, 100 mM Tris-HCl, 20% (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 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→44.94 Å / Num. obs: 51614 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 43.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 15.3 % / Rmerge(I) obs: 1.425 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2833 / CC1/2: 0.86 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8GQ9 Resolution: 2.41→44.94 Å / SU ML: 0.2998 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.8968 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: 55.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→44.94 Å
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Refine LS restraints |
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LS refinement shell |
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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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