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- PDB-7zkg: C-Methyltransferase PsmD from Streptomyces griseofuscus with boun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zkg | ||||||
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Title | C-Methyltransferase PsmD from Streptomyces griseofuscus with bound cofactor (crystal form 2) | ||||||
![]() | Methyltransferase | ||||||
![]() | TRANSFERASE / Rossmann fold / Cap domain / indole C3-methylation / S-adenosyl methionine | ||||||
Function / homology | Methyltransferase domain 25 / Methyltransferase domain / biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weiergraeber, O.H. / Amariei, D.A. / Pozhydaieva, N. / Pietruszka, J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD-Crystal Structure, Catalytic Mechanism, and Preparative Applications Authors: Amariei, D.A. / Pozhydaieva, N. / David, B. / Schneider, P. / Classen, T. / Gohlke, H. / Weiergraber, O.H. / Pietruszka, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244.7 KB | Display | ![]() |
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PDB format | ![]() | 176.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922.7 KB | Display | ![]() |
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Full document | ![]() | 924.8 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zgtC ![]() 7zkhC ![]() 1wznS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30780.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-MPD / ( #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: SOKALAN CP 42, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→56.32 Å / Num. obs: 41427 / % possible obs: 100 % / Redundancy: 39.29 % / Biso Wilson estimate: 61.18 Å2 / CC1/2: 1 / Rrim(I) all: 0.122 / Net I/σ(I): 28.55 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 40.66 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 3019 / CC1/2: 0.54 / Rrim(I) all: 4.586 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WZN Resolution: 2.3→56.32 Å / SU ML: 0.3018 / Cross valid method: FREE R-VALUE / Phase error: 24.4999 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: 76.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→56.32 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 | Refine-ID: X-RAY DIFFRACTION
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