+Open data
-Basic information
Entry | Database: PDB / ID: 3dss | ||||||
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Title | Crystal structure of RabGGTase(DELTA LRR; DELTA IG) | ||||||
Components |
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Keywords | TRANSFERASE / protein prenylation / Metal-binding / Prenyltransferase / Zinc / 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: 1.8 Å | ||||||
Authors | Guo, Z. / Yu, S. / Goody, R.S. / Alexandrov, K. / Blankenfeldt, W. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation Authors: Guo, Z. / Wu, Y.-W. / Das, D. / Delon, C. / Cramer, J. / Yu, S. / Thuns, S. / Lupilova, N. / Waldmann, H. / Brunsveld, L. / Goody, R.S. / Alexandrov, K. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dss.cif.gz | 284.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dss.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/3dss ftp://data.pdbj.org/pub/pdb/validation_reports/ds/3dss | HTTPS FTP |
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-Related structure data
Related structure data | 3dstC 3dsuC 3dsvC 3dswC 3dsxC 1ltxS C: citing same article (ref.) 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
#1: Protein | Mass: 38441.598 Da / Num. of mol.: 1 / Fragment: PFTA domains, UNP residues 1-237 and 353-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Description: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a Gene: Rabggta, Ggta / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (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) Description: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a Gene: Rabggtb, Ggtb / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) References: UniProt: Q08603, protein geranylgeranyltransferase type II | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, 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: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2006 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 64818 / Num. obs: 64333 / % possible obs: 99.3 % / Observed criterion σ(I): 5 / Redundancy: 4.6 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.063 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 9571 / Rsym value: 0.275 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LTX Resolution: 1.8→29.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.356 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS-REFINEMENT WAS USED
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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: 17.742 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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