+Open data
-Basic information
Entry | Database: PDB / ID: 3c72 | ||||||
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Title | Engineered RabGGTase in complex with a peptidomimetic inhibitor | ||||||
Components | (Geranylgeranyl transferase type-2 subunit ...) x 2 | ||||||
Keywords | TRANSFERASE / peptide inhibitor / Rab prenylation / Metal-binding / Prenyltransferase / Phosphoprotein | ||||||
Function / homology | Function and homology information isoprenoid binding / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / protein geranylgeranyltransferase type II / RAB geranylgeranylation / Rab-protein geranylgeranyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / small GTPase binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Guo, Z. / Wu, Y.W. / Tan, K.T. / Bon, R.S. / Guiu-Rozas, E. / Delon, C. / Nguyen, U.T. / Wetzel, S. / Arndt, S. / Goody, R.S. ...Guo, Z. / Wu, Y.W. / Tan, K.T. / Bon, R.S. / Guiu-Rozas, E. / Delon, C. / Nguyen, U.T. / Wetzel, S. / Arndt, S. / Goody, R.S. / Blankenfeldt, W. / Alexandrov, K. / Waldmann, H. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008 Title: Development of selective RabGGTase inhibitors and crystal structure of a RabGGTase-inhibitor complex. Authors: Guo, Z. / Wu, Y.W. / Tan, K.T. / Bon, R.S. / Guiu-Rozas, E. / Delon, C. / Nguyen, T.U. / Wetzel, S. / Arndt, S. / Goody, R.S. / Blankenfeldt, W. / Alexandrov, K. / Waldmann, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c72.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c72.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/3c72 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/3c72 | HTTPS FTP |
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-Related structure data
Related structure data | 1ltxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Geranylgeranyl transferase type-2 subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38693.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rabggta, Ggta / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q08602, protein geranylgeranyltransferase type II |
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#2: Protein | Mass: 36892.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rabggtb, Ggtb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q08603, protein geranylgeranyltransferase type II |
-Non-polymers , 4 types, 194 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-CX1 / |
#6: 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: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 14% (w/v) PEG 3350, 0.2 M Ca-Acetate, 0.1 M HEPES, cocrystallization with 5 mM inhibitor, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: Si(111) monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 31830 / % possible obs: 99.7 % / Observed criterion σ(I): 4.7 / Redundancy: 5.7 % / Biso Wilson estimate: 50 Å2 / Rsym value: 5.2 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 3742 / Rsym value: 40.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LTX Resolution: 2.3→19.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.187 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS bodies have been assigned with TLSMD
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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: 31.217 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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