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Yorodumi- PDB-2py6: Crystal structure of Methyltransferase FkbM (YP_546752.1) from Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2py6 | ||||||
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Title | Crystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution | ||||||
Components | Methyltransferase FkbM | ||||||
Keywords | TRANSFERASE / YP_546752.1 / Methyltransferase FkbM / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methylobacillus flagellatus KT (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2py6.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2py6.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 2py6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2py6_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
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Full document | 2py6_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 2py6_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2py6_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/2py6 ftp://data.pdbj.org/pub/pdb/validation_reports/py/2py6 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46512.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria) Species: Methylobacillus flagellatus / Strain: KT, DSM 6875 / Gene: YP_546752.1, Mfla_2648 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 References: UniProt: Q1GXX6, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 5 types, 386 molecules
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: NANODROP, 0.214M Ammonium nitrate, 14.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97926, 0.97891 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2007 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.15→29.788 Å / Num. obs: 29426 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.24 % / Biso Wilson estimate: 24.43 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.69 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.15→29.788 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.375 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.171 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CHLORIDE ION, ETHYLENE GLYCOL, POLYETHYLENE GLYCOL-3350 (PEG) AND ONE UNKNOWN LIGAND (UNL) ARE MODELED IN THE STRUCTURE. THE UNKNOWN LIGAND IS CLOSE TO RESIDUES 259 AND 342. 5. RESIDUES 1-13 AND 300-319 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 6. THERE IS A RAMACHANDRAN VIOLATION ON RESIUDE 112 WITH CLEAR DENSITY SUPPORT.
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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 mean: 28.849 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→29.788 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / 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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