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Yorodumi- PDB-3pz3: Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pz3 | ||||||
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Title | Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS-analogue 14 | ||||||
Components | (Geranylgeranyl transferase type-2 subunit ...) x 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / fusion protein / chimera protein / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pz3.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pz3.ent.gz | 223.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/3pz3 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/3pz3 | HTTPS FTP |
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-Related structure data
Related structure data | 3pz1C 3pz2C 3pz4C 3dssS 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
-Geranylgeranyl transferase type-2 subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38498.652 Da / Num. of mol.: 1 / Fragment: UNP residues 1-237 and 353-441 Source method: isolated from a genetically manipulated source Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a Source: (gene. exp.) Rattus norvegicus (Norway rat) / 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: 36760.965 Da / Num. of mol.: 1 / Fragment: UNP residues 10-339 Source method: isolated from a genetically manipulated source Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a Source: (gene. exp.) Rattus norvegicus (Norway rat) / 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 |
-Non-polymers , 4 types, 336 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-PZ3 / |
#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: 47.01 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M 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: 0.977 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 31, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 48077 / Num. obs: 47598 / % possible obs: 99 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.041 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 6416 / Rsym value: 0.354 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DSS Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.846 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 36.218 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 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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