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Yorodumi- PDB-3h2b: Crystal structure of the SAM-dependent methyltransferase cg3271 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h2b | ||||||
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Title | Crystal structure of the SAM-dependent methyltransferase cg3271 from Corynebacterium glutamicum in complex with S-adenosyl-L-homocysteine and pyrophosphate. Northeast Structural Genomics Consortium Target CgR113A | ||||||
Components | SAM-dependent methyltransferase | ||||||
Keywords | TRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Methyltransferase | ||||||
Function / homology | Vaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PYROPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / : Function and homology information | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be published Title: Northeast Structural Genomics Consortium Target CgR113A Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h2b.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h2b.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 3h2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h2b_validation.pdf.gz | 1006.9 KB | Display | wwPDB validaton report |
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Full document | 3h2b_full_validation.pdf.gz | 1011.7 KB | Display | |
Data in XML | 3h2b_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 3h2b_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/3h2b ftp://data.pdbj.org/pub/pdb/validation_reports/h2/3h2b | 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 | AUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE. |
-Components
#1: Protein | Mass: 22248.203 Da / Num. of mol.: 2 / Fragment: UNP residues 58-252 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Strain: DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 / Gene: cg3271 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6M1Q8 #2: Chemical | #3: Chemical | ChemComp-PPV / | #4: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl pH 7.5. Reservoir solution: 100mM Sodium cacodylate pH 6.5, 25% PEG 8000, 200mM Ammonium sulfate, MICROBATCH UNDER OIL, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97869 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 50463 / Num. obs: 50463 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.133 / Net I/σ(I): 14.14 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.62 / Num. unique all: 5044 / Rsym value: 0.49 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 321463.094 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing. Program XtalView has also been used in refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.364 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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