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Yorodumi- PDB-5v7p: Atomic structure of the eukaryotic intramembrane Ras methyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v7p | ||||||
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Title | Atomic structure of the eukaryotic intramembrane Ras methyltransferase ICMT (isoprenylcysteine carboxyl methyltransferase), in complex with a monobody | ||||||
Components |
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Keywords | TRANSFERASE / membrane protein / membrane enzyme / methyltransferase / LCP | ||||||
Function / homology | Function and homology information protein-S-isoprenylcysteine O-methyltransferase / protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity / C-terminal protein methylation / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Tribolium castaneum (red flour beetle) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å | ||||||
Authors | Long, S.B. / Diver, M.M. / Pedi, L. / Koide, A. / Koide, S. | ||||||
Citation | Journal: Nature / Year: 2018 Title: Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Authors: Diver, M.M. / Pedi, L. / Koide, A. / Koide, S. / Long, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v7p.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v7p.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 5v7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v7p_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5v7p_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 5v7p_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 5v7p_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/5v7p ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v7p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 32857.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC013078 / Production host: Pichia (fungus) References: UniProt: D6WJ77, protein-S-isoprenylcysteine O-methyltransferase |
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#2: Protein | Mass: 10135.358 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 5 types, 117 molecules
#3: Chemical | ChemComp-SAH / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-D10 / #6: Chemical | ChemComp-MPG / [( #7: 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: 3.05 Å3/Da / Density % sol: 59.72 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 40/60% (v/v ICMT:9.9 monoacylgylcerol) 30% PEG 400 100 mM NaCl 100 mM Na HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 9, 2015 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31 Å / Num. obs: 23204 / % possible obs: 97.2 % / Redundancy: 11.2 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.863 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.062 / Χ2: 1.01 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1197 / CC1/2: 0.547 / Rpim(I) all: 0.295 / Χ2: 0.95 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: SIRAS / Resolution: 2.3→29.772 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.3 / Phase error: 22.02 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.772 Å
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Refine LS restraints |
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LS refinement shell |
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