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Yorodumi- PDB-4k0b: Crystal structure of S-Adenosylmethionine synthetase from Sulfolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k0b | ||||||
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Title | Crystal structure of S-Adenosylmethionine synthetase from Sulfolobus solfataricus complexed with SAM and PPi | ||||||
Components | S-adenosylmethionine synthase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro | ||||||
Function / homology | Function and homology information methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.39 Å | ||||||
Authors | Wang, F. / Hurley, K.A. / Helmich, K.E. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT from Sulfolobus solfataricus. Authors: Wang, F. / Singh, S. / Zhang, J. / Huber, T.D. / Helmich, K.E. / Sunkara, M. / Hurley, K.A. / Goff, R.D. / Bingman, C.A. / Morris, A.J. / Thorson, J.S. / Phillips, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k0b.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k0b.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k0b_validation.pdf.gz | 790.1 KB | Display | wwPDB validaton report |
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Full document | 4k0b_full_validation.pdf.gz | 797.2 KB | Display | |
Data in XML | 4k0b_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 4k0b_validation.cif.gz | 53.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/4k0b ftp://data.pdbj.org/pub/pdb/validation_reports/k0/4k0b | HTTPS FTP |
-Related structure data
Related structure data | 4hpvC 4l2zC 4l7iC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45330.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: mat, Ssol_1180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980S9, methionine adenosyltransferase |
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-Non-polymers , 5 types, 601 molecules
#2: Chemical | #3: Chemical | ChemComp-DPO / | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-SAM / | #6: 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: 4.04 Å3/Da / Density % sol: 69.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Protein Solution (9.0 mg/ml protein in 25mM Tris pH 8.0, 5mM ADP, 10mM Methione, 10mM MgCl2, 50mM KCl and 5mM DTT) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate ...Details: Protein Solution (9.0 mg/ml protein in 25mM Tris pH 8.0, 5mM ADP, 10mM Methione, 10mM MgCl2, 50mM KCl and 5mM DTT) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 5.6) Cryoprotected with 25% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→50 Å / Num. all: 217046 / Num. obs: 215744 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.395 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.175 / Net I/σ(I): 8.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.39→49.42 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8621 / SU ML: 0.24 / σ(F): 1.33 / Phase error: 20.46 / 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: 217.65 Å2 / Biso mean: 38.3032 Å2 / Biso min: 12.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→49.42 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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