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Yorodumi- PDB-3dra: Candida albicans protein geranylgeranyltransferase-I complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dra | ||||||
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Title | Candida albicans protein geranylgeranyltransferase-I complexed with GGPP | ||||||
Components |
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Keywords | TRANSFERASE / geranylgeranyltrasferase / geranylgeranyltransferase type-I / GGTase / GGTase-I / PGGT / prenyltransferase / farnesyltransferase / prenylation / geranylgeranylpyrophosphate / GGPP / geranylgeranyl diphosphate / Candida / Candida albicans | ||||||
Function / homology | Function and homology information peptide pheromone maturation / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / protein geranylgeranylation Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hast, M.A. / Beese, L.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structure of protein geranylgeranyltransferase-I from the human pathogen Candida albicans complexed with a lipid substrate. Authors: Hast, M.A. / 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 | 3dra.cif.gz | 160.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dra.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dra_validation.pdf.gz | 847.2 KB | Display | wwPDB validaton report |
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Full document | 3dra_full_validation.pdf.gz | 853.7 KB | Display | |
Data in XML | 3dra_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 3dra_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/3dra ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3dra | HTTPS FTP |
-Related structure data
Related structure data | |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36659.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: RAM2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y765, protein farnesyltransferase, protein geranylgeranyltransferase type I |
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#2: Protein | Mass: 45665.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: CDC43 / Production host: Escherichia coli (E. coli) |
-Non-polymers , 4 types, 474 molecules
#3: Chemical | ChemComp-B3P / |
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#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-GRG / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | ACCORDING TO THE AUTHORS THE GENES FOR THE SUBUNITS OF THE ENZYME FROM THIS ORGANISM EXHIBIT ...ACCORDING TO THE AUTHORS THE GENES FOR THE SUBUNITS OF THE ENZYME FROM THIS ORGANISM EXHIBIT SIGNIFICAN |
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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: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 1500, propionate-cacodylate-bis-tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 63895 / % possible obs: 98.17 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 76.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.64 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.008 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 3.1 / σ(I): -3 / ESU R: 0.145 / ESU R Free: 0.135 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.285 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20
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