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- PDB-1tny: Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tny | ||||||
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Title | Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a FREKKFFCAIL Peptide Derived from the Heterotrimeric G Protein Gamma-2 Subunit | ||||||
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![]() | TRANSFERASE / GGTase-I / geranylgeranyltransferase type-I / geranylgeranyl transferase / prenyltransferase / CaaX / heterotrimeric G protein / Lipid modification / prenylation / substrate selectivity | ||||||
Function / homology | ![]() Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / heterocyclic compound binding / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / : / positive regulation of cell cycle / response to cytokine / response to organic cyclic compound / receptor tyrosine kinase binding / microtubule binding / molecular adaptor activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | S Reid, T. / Terry, K.L. / Casey, P.J. / Beese, L.S. | ||||||
![]() | ![]() Title: Crystallographic analysis of CaaX prenyltransferases complexed with substrates defines rules of protein substrate selectivity. Authors: Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 811 KB | Display | ![]() |
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PDB format | ![]() | 670.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 152.4 KB | Display | |
Data in CIF | ![]() | 207.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tn6C ![]() 1tn7C ![]() 1tn8C ![]() 1tnbC ![]() 1tnoC ![]() 1tnuC ![]() 1tnzC ![]() 1n4qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 44098.145 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q04631, protein geranylgeranyltransferase type I #2: Protein | Mass: 42466.176 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P53610, protein geranylgeranyltransferase type I |
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-Protein/peptide , 1 types, 6 molecules MNOPQR
#3: Protein/peptide | Mass: 1404.740 Da / Num. of mol.: 6 / Fragment: C-terminal residues 61-71 / Source method: obtained synthetically Details: THE SUBSTRATE PEPTIDE WAS CHEMICALLY SYNTHESIZED. The sequence of this peptide naturally exists in Homo sapiens (Human). |
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-Non-polymers , 5 types, 1024 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MGM.gif)
![](data/chem/img/MES.gif)
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![](data/chem/img/CL.gif)
![](data/chem/img/MGM.gif)
![](data/chem/img/MES.gif)
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#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-MGM / #7: Chemical | ChemComp-MES / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.5 Å3/Da / Density % sol: 77.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 1.3 M ammonium sulfate, 175 mM NaCitrate pH 6.5, 100 mM MES pH 6.3, 20 mM DTT, 1uM ZnCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2002 Details: Elliptically bent mirror/sagittal focusing second monochromator crystal |
Radiation | Monochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 252331 / Num. obs: 250142 / % possible obs: 94.1 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 3 % / Biso Wilson estimate: 53.7 Å2 / Rsym value: 0.058 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.5 / Num. unique all: 21852 / Rsym value: 0.247 / % possible all: 82.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1N4Q Resolution: 2.7→29.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 219354.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -0.5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.4204 Å2 / ksol: 0.364459 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
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Xplor file |
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