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Yorodumi- PDB-2a22: Structure of Vacuolar Protein Sorting 29 from Cryptosporidium Parvum -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a22 | ||||||
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Title | Structure of Vacuolar Protein Sorting 29 from Cryptosporidium Parvum | ||||||
Components | vacuolar protein sorting 29Vacuole | ||||||
Keywords | PROTEIN TRANSPORT / VACUOLAR PROTEIN SORTING PROTEIN / ALPHA-BETA-BETA-ALPHA SANDWICH / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information retromer complex / retrograde transport, endosome to Golgi / phosphoprotein phosphatase activity / protein transport / cytosol Similarity search - Function | ||||||
Biological species | Cryptosporidium parvum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.198 Å | ||||||
Authors | Brokx, S. / Zhao, Y. / Alam, Z. / Lew, J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. ...Brokx, S. / Zhao, Y. / Alam, Z. / Lew, J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2007 Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a22.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a22.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/2a22 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/2a22 | HTTPS FTP |
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-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C 1w24S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The quaternary structure is a monomer |
-Components
#1: Protein | Mass: 23777.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5CYJ7 #2: Water | ChemComp-HOH / | |
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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: 2.49 Å3/Da / Density % sol: 36.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 22% w/v PEG 400, 100 mM sodium citrate pH 5.6, 200 mM ammonium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.198→28.9 Å / Num. all: 24958 / Num. obs: 24958 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 22.89 |
Reflection shell | Resolution: 2.198→2.28 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.45 / Num. unique all: 2440 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W24 Resolution: 2.198→28.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.689 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.181 / 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: 27.318 Å2
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Refinement step | Cycle: LAST / Resolution: 2.198→28.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.198→2.255 Å / Total num. of bins used: 20
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