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Yorodumi- PDB-6yjw: Structure of Fragaria ananassa O-methyltransferase crystallized w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yjw | ||||||
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Title | Structure of Fragaria ananassa O-methyltransferase crystallized with PAS polypeptide | ||||||
Components | O-methyltransferase | ||||||
Keywords | TRANSFERASE / PAS polypeptide / P/A200 / precipitant / proline-alanine rich sequence / protein crystallization | ||||||
Function / homology | Function and homology information caffeate O-methyltransferase / lignin biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | Fragaria ananassa (strawberry) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Schiefner, A. / Skerra, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Proline/alanine-rich sequence (PAS) polypeptides as an alternative to PEG precipitants for protein crystallization. Authors: Schiefner, A. / Walser, R. / Gebauer, M. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yjw.cif.gz | 297.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yjw.ent.gz | 239.1 KB | Display | PDB format |
PDBx/mmJSON format | 6yjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yjw_validation.pdf.gz | 767.4 KB | Display | wwPDB validaton report |
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Full document | 6yjw_full_validation.pdf.gz | 773 KB | Display | |
Data in XML | 6yjw_validation.xml.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/6yjw ftp://data.pdbj.org/pub/pdb/validation_reports/yj/6yjw | HTTPS FTP |
-Related structure data
Related structure data | 6yjxC 6i71S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 13 - 365 / Label seq-ID: 10 - 362
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-Components
#1: Protein | Mass: 39718.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fragaria ananassa (strawberry) / Gene: omt1 / Plasmid: pASK75 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9M602 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.01 Å3/Da / Density % sol: 59.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 12.5 % (w/v) PA200 0.1 M Hepes/NaOH 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 30, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→34.78 Å / Num. obs: 56709 / % possible obs: 99.9 % / Redundancy: 8.894 % / Biso Wilson estimate: 38.355 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.107 / Χ2: 0.985 / Net I/σ(I): 18.29 / Num. measured all: 504350 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I71 Resolution: 2.1→34.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.354 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.142 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.16 Å2 / Biso mean: 34.811 Å2 / Biso min: 16.59 Å2
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Refinement step | Cycle: final / Resolution: 2.1→34.78 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 10904 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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