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Yorodumi- PDB-8bid: O-Methyltransferase Plu4890 (mutant H229N) in complex with SAH an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bid | ||||||
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Title | O-Methyltransferase Plu4890 (mutant H229N) in complex with SAH and AQ-270a | ||||||
Components | methyltransferase Plu4890 H229N mutant | ||||||
Keywords | TRANSFERASE / methyltransferase / polyketide / anthraquinone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Huber, E.M. / Groll, M. | ||||||
Funding support | 1items
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Citation | Journal: Structure / Year: 2023 Title: A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Authors: Huber, E.M. / Kreling, L. / Heinrich, A.K. / Dunnebacke, M. / Pothig, A. / 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 | 8bid.cif.gz | 563.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bid.ent.gz | 459.9 KB | Display | PDB format |
PDBx/mmJSON format | 8bid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bid_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8bid_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8bid_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 8bid_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/8bid ftp://data.pdbj.org/pub/pdb/validation_reports/bi/8bid | HTTPS FTP |
-Related structure data
Related structure data | 8bgtSC 8bgxC 8bgyC 8bgzC 8bh0C 8bibC 8bicC 8bieC 8bifC 8bigC 8bihC 8biiC 8bijC 8birC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36526.480 Da / Num. of mol.: 4 / Mutation: H229N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L9JR93 |
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-Non-polymers , 6 types, 585 molecules
#2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-QPF / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-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: 2.81 Å3/Da / Density % sol: 56.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25 % PEG4000 |
-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: Feb 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→49 Å / Num. obs: 159145 / % possible obs: 97.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.75→1.85 Å / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / Num. unique obs: 24786 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8BGT Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.915 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 641.01 Å2 / Biso mean: 33.681 Å2 / Biso min: 17.16 Å2
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Refinement step | Cycle: final / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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