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Yorodumi- PDB-1o9t: Methionine adenosyltransferase complexed with both substrates ATP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o9t | ||||||
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Title | Methionine adenosyltransferase complexed with both substrates ATP and methionine | ||||||
Components | S-ADENOSYLMETHIONINE SYNTHETASE | ||||||
Keywords | TRANSFERASE / ADENOSYLTRANSFERASE / ATP BINDING / METHIONINE BINDING / ONE-CARBON METABOLISM / MAGNESIUM / POTASSIUM / METAL-BINDING / MULTIGENE FAMILY / ATP-BINDING | ||||||
Function / homology | Function and homology information Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / ADP binding ...Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / ADP binding / nuclear matrix / one-carbon metabolic process / protein-containing complex assembly / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Gonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Sanz-Aparicio, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structures of Methionine Adenosyltransferase Complexed with Substrates and Products Reveal the Methionine-ATP Recognition and Give Insights Into the Catalytic Mechanism Authors: Gonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Guillerm, D. / Guillerm, G. / Sanz-Aparicio, J. #1: Journal: J.Mol.Biol. / Year: 2000 Title: The Crystal Structure of Tetrameric Methionine Adenosyltransferase Fom Rat Liver Reveals the Methionine Binding Site Authors: Gonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Alvarez, L. / Garrido, F. / Sufrin, J.R. / Sanz-Aparicio, J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9t.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9t.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 1o9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9t ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9t | HTTPS FTP |
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-Related structure data
Related structure data | 1o90C 1o92C 1o93C 1qm4S C: citing same article (ref.) S: Starting model for refinement |
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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 oper: (Code: given Matrix: (-0.7849, -0.2307, 0.575), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43637.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: LIVER / Plasmid: PSSRL-T7N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13444, methionine adenosyltransferase |
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-Non-polymers , 6 types, 185 molecules
#2: Chemical | ChemComp-MET / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ATP / | #7: Water | ChemComp-HOH / | |
-Details
Compound details | CATALYSES THE REACTION BETWEEN ATP AND L-METHIONINESequence details | THE SWISS-PROT ACCESSION FOR THIS ENTRY P13444 HAS A RESIDUE ASN AT POSITION 345. THE DEPOSITORS ...THE SWISS-PROT ACCESSION FOR THIS ENTRY P13444 HAS A RESIDUE ASN AT POSITION 345. THE DEPOSITORS | |
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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: 3.2 Å3/Da / Density % sol: 61 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 16% PEG 10000, 10MM L-METHIONINE, 100MM HEPES PH=7.5 (SOAKING IN 30 MM ATP SOLUTION), pH 7.50 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→44.7 Å / Num. obs: 27747 / % possible obs: 97.5 % / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Rsym value: 0.074 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.76→2.92 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.443 / % possible all: 97.9 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 27790 / Redundancy: 4.1 % / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å / % possible obs: 97.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QM4 Resolution: 2.9→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters | Biso mean: 37.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 25 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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