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Yorodumi- PDB-1tnz: Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tnz | ||||||
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Title | Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a RRCVLL Peptide Derived from Cdc42 splice isoform-2 | ||||||
Components |
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Keywords | TRANSFERASE / GGTase-I / geranylgeranyltransferase type-I / geranylgeranyl transferase / prenyltransferase / CaaX / Cdc42 / Lipid modification / prenylation / substrate selectivity | ||||||
Function / homology | Function and homology information 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tnz.cif.gz | 791.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tnz.ent.gz | 655.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tnz_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1tnz_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1tnz_validation.xml.gz | 144.3 KB | Display | |
Data in CIF | 1tnz_validation.cif.gz | 194.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/1tnz ftp://data.pdbj.org/pub/pdb/validation_reports/tn/1tnz | HTTPS FTP |
-Related structure data
Related structure data | 1tn6C 1tn7C 1tn8C 1tnbC 1tnoC 1tnuC 1tnyC 1n4qS 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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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.) Rattus norvegicus (Norway rat) / Gene: FNTA / Production host: Spodoptera frugiperda (fall armyworm) 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.) Rattus norvegicus (Norway rat) / Gene: PGGT1B / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P53610, protein geranylgeranyltransferase type I |
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-Protein/peptide , 1 types, 6 molecules MNOPQR
#3: Protein/peptide | Mass: 760.992 Da / Num. of mol.: 6 / Fragment: C-terminal residues 186-191 / 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, 272 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-MGM / #6: Chemical | #7: Chemical | ChemComp-MES / | #8: 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: 5.5 Å3/Da / Density % sol: 77.4 % |
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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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2003 / Details: Pt-coated toroidal Si mirror |
Radiation | Monochromator: Si crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 212963 / Num. obs: 197897 / % possible obs: 91.4 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 2.5 % / Biso Wilson estimate: 41.3 Å2 / Rsym value: 0.067 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.295 / % possible all: 81 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdn entry 1N4Q Resolution: 2.9→29.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 377045.61 / 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: 58.753 Å2 / ksol: 0.35749 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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