+Open data
-Basic information
Entry | Database: PDB / ID: 7wzf | ||||||
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Title | Structural and mechanism analysis of YunM | ||||||
Components | YunM | ||||||
Keywords | TRANSFERASE / Linaridin Methyltransferase | ||||||
Function / homology | S-ADENOSYL-L-HOMOCYSTEINE Function and homology information | ||||||
Biological species | Streptomyces yunnanensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Duan, S.Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structural and mechanism analysis of YunM Authors: Duan, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wzf.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wzf.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wzf_validation.pdf.gz | 724.2 KB | Display | wwPDB validaton report |
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Full document | 7wzf_full_validation.pdf.gz | 725.1 KB | Display | |
Data in XML | 7wzf_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 7wzf_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/7wzf ftp://data.pdbj.org/pub/pdb/validation_reports/wz/7wzf | HTTPS FTP |
-Related structure data
Related structure data | 4hh4S S: Starting model for refinement |
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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
#1: Protein | Mass: 29806.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The sequence has been deposited to NCBI with accession code WP_073444433.1, and contains tag sequence MGSSHHHHHHSSGLVPRGSH at N-terminal. Source: (gene. exp.) Streptomyces yunnanensis (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-SAH / |
#3: 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: 3.31 Å3/Da / Density % sol: 62.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Under the condition of 2000 mM ammonium sulfate, 100 mM CAPS/ sodium hydroxide pH 10.5, 200 mM lithium sulfate an initial crystallization condition was identified over 3 weeks and was ...Details: Under the condition of 2000 mM ammonium sulfate, 100 mM CAPS/ sodium hydroxide pH 10.5, 200 mM lithium sulfate an initial crystallization condition was identified over 3 weeks and was subsequently optimized to yield well-diffracting crystals. Final optimized conditions for YunM with SAM contained 1800 mM ammonium sulfate, 100 mM CAPS/sodium hydroxide pH 10.4, 100 mM lithium sulfate, and yielded square crystals |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 73359 / % possible obs: 99.7 % / Redundancy: 1.1 % / CC1/2: 0.992 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 7005 / CC1/2: 0.836 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HH4 Resolution: 1.4→23.33 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.25 / Stereochemistry target values: ML
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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 max: 45.89 Å2 / Biso mean: 17.5102 Å2 / Biso min: 8.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→23.33 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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