[English] 日本語
Yorodumi- PDB-3pz4: Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pz4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10) in complex with BMS3 and lipid substrate FPP | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / regulation of fibroblast proliferation / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / farnesyltranstransferase activity / microtubule associated complex / 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 / wound healing / response to organic cyclic compound / lipid metabolic process / receptor tyrosine kinase binding / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / 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: 2.1 Å | ||||||
Authors | Guo, Z. / Bon, R.S. / Stigter, E.A. / Waldmann, H. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2011 Title: Structure-Guided Development of Selective RabGGTase Inhibitors. Authors: Bon, R.S. / Guo, Z. / Stigter, E.A. / Wetzel, S. / Menninger, S. / Wolf, A. / Choidas, A. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pz4.cif.gz | 321.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pz4.ent.gz | 262.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pz4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3pz4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3pz4_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 3pz4_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/3pz4 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/3pz4 | HTTPS FTP |
-Related structure data
Related structure data | 3pz1C 3pz2C 3pz3C 3eu5S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44293.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET30a Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta, Ggta, Rabggta / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I |
---|---|
#2: Protein | Mass: 47618.148 Da / Num. of mol.: 1 / Fragment: UNP residues 2-427 Source method: isolated from a genetically manipulated source Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET30a Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb, Ggtb, Rabggtb / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) / References: UniProt: Q02293, protein farnesyltransferase |
-Non-polymers , 4 types, 309 molecules
#3: Chemical | ChemComp-ZN / |
---|---|
#4: Chemical | ChemComp-FPP / |
#5: Chemical | ChemComp-3PZ / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.11 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% (w/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 67245 / Num. obs: 67104 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 6.2 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.06 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 8682 / Rsym value: 0.359 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EU5 Resolution: 2.1→29.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.485 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.501 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.91 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|