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Yorodumi- PDB-1ozv: Crystal structure of the SET domain of LSMT bound to Lysine and AdoHcy -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ozv | ||||||
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Title | Crystal structure of the SET domain of LSMT bound to Lysine and AdoHcy | ||||||
Components | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast | ||||||
Keywords | TRANSFERASE / SET DOMAIN / LYSINE N-METHYLATION / MULTIPLE METHYLATION / PHOTOSYNTHESIS / POST-TRANSLATIONAL MODIFICATION | ||||||
Function / homology | Function and homology information [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase / [fructose-bisphosphate aldolase]-lysine N-methyltransferase / [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity / protein-lysine N-methyltransferase activity / chloroplast / methylation Similarity search - Function | ||||||
Biological species | Pisum sativum (garden pea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Trievel, R.C. / Flynn, E.M. / Houtz, R.L. / Hurley, J.H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT Authors: Trievel, R.C. / Flynn, E.M. / Houtz, R.L. / Hurley, J.H. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE ...SEQUENCE AUTHORS INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE THAT WAS ENGINEERED INTO THE ENZYME AFTER LEU 482. AFTER CLEAVAGE, THESE SIX RESIDUES WERE LEFT ON THE C-TERMINUS OF THIS CONSTRUCT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ozv.cif.gz | 286.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ozv.ent.gz | 230.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ozv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ozv_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1ozv_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1ozv_validation.xml.gz | 60.7 KB | Display | |
Data in CIF | 1ozv_validation.cif.gz | 84.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/1ozv ftp://data.pdbj.org/pub/pdb/validation_reports/oz/1ozv | HTTPS FTP |
-Related structure data
Related structure data | 1p0yC 1mlvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 50629.160 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q43088, [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase #2: Chemical | #3: Chemical | #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: 4.38 Å3/Da / Density % sol: 71.67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.95-1.10 M Sodium Acetate, 100 mM Lysine Acetate, 1 mM TCEP, 400 uM S-adenosylhomocysteine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 2, 2002 / Details: Osmic Confocal Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 80333 / Num. obs: 79741 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 39.3 Å2 / Rsym value: 0.056 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.65→2.74 Å / Mean I/σ(I) obs: 2.51 / Num. unique all: 7902 / Rsym value: 0.494 / % possible all: 99 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 99 % / Num. unique obs: 7902 / Rmerge(I) obs: 0.494 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1MLV Resolution: 2.65→29.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 612033.97 / Data cutoff high rms absF: 612033.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.51 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.2167 Å2 / ksol: 0.339194 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→29.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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