+Open data
-Basic information
Entry | Database: PDB / ID: 1fkm | ||||||
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Title | CRYSTAL STRUCTURE OF THE YPT/RAB-GAP DOMAIN OF GYP1P | ||||||
Components | PROTEIN (GYP1P) | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / GAP / YPT/RAB PROTEIN / VESICULAR TRAFFICKING / ENDOCYTOSIS / HYDROLASE / GTPASE ACTIVATION / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information Golgi stack / vesicle-mediated transport / GTPase activator activity / Golgi apparatus / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Rak, A. / Fedorov, R. / Alexandrov, K. / Albert, S. / Goody, R.S. / Gallwitz, D. / Scheidig, A.J. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins. Authors: Rak, A. / Fedorov, R. / Alexandrov, K. / Albert, S. / Goody, R.S. / Gallwitz, D. / Scheidig, A.J. #1: Journal: Embo J. / Year: 1999 Title: Identification of the Catalytic Domains and their Functionally Critical Arginine Residues of Two Yeast GTPase-activating Proteins Specific for Ypt/Rab Transport GTPases Authors: Albert, S. / Will, E. / Gallwitz, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fkm.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fkm.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/1fkm ftp://data.pdbj.org/pub/pdb/validation_reports/fk/1fkm | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 47324.641 Da / Num. of mol.: 1 / Fragment: YPT/RAB-GAP DOMAIN, RESIDUES 248-637 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Description: GENOMIC DNA / Plasmid: PET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: Q08484 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG MME 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 237598 / Num. obs: 33503 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.242 / Num. unique all: 3020 / % possible all: 97.1 | ||||||||||||||||||
Reflection | *PLUS Num. measured all: 237598 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 97.1 % / Mean I/σ(I) obs: 6.5 |
-Processing
Software |
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Refinement | Resolution: 1.9→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 852619.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: For the first crystal, EMBL/DESY, HAMBURG, BEAMLINE BW6 (MAD experiment): Se L1 (0.9790 A) dmin = 20.0-2.35 No. of Reflections = 461421 No. of Unique Reflections = 36326 Completeness = 99.2 ...Details: For the first crystal, EMBL/DESY, HAMBURG, BEAMLINE BW6 (MAD experiment): Se L1 (0.9790 A) dmin = 20.0-2.35 No. of Reflections = 461421 No. of Unique Reflections = 36326 Completeness = 99.2 I/SIGMA (%) = 27.5 Rsym = 6.8; Se L2 (0.9795 A) dmin = 20.0-2.35 No. of Reflections = 458264 No. of Unique Reflections = 36412 Completeness = 99.3 I/SIGMA (%) = 27.0 Rsym = 7.1' Se L3 (0.9200 A) dmin = 20.0-2.7 No. of Reflections = 275885 No. of Unique Reflections = 23838 Completeness = 98.4 I/SIGMA (%) = 38.8 Rsym = 5.5 Observed diffraction ratios : L1 x L1 = 0.0677 L1 x L2 = 0.0360 L1 x L3 = 0.0470 L2 x L2 = 0.0558 L2 x L3 = 0.0520 L3 x L3 =0.0466 For the second crystal, EMBL/DESY, HAMBURG, BEAMLINE BW7A (high-resolution data set): Se L4 (0.8428 A) dmin = 6.0-1.9 No. of Reflections = 237598 No. of Unique Reflections = 33502 Completeness = 91.2 I/SIGMA (%) = 14.4 Rsym = 9.4 (24.2)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 82.45 Å2 / ksol: 0.607 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.01 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.252 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.223 |