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Yorodumi- PDB-2ghi: Crystal Structure of Plasmodium yoelii Multidrug Resistance Protein 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ghi | ||||||
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Title | Crystal Structure of Plasmodium yoelii Multidrug Resistance Protein 2 | ||||||
Components | transport protein | ||||||
Keywords | TRANSPORT PROTEIN / Plasmodium yoelii / Multidrug Resistance Protein / MDR / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ATPase-coupled transmembrane transporter activity / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Plasmodium yoelii yoelii str. 17XNL (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dong, A. / Gao, M. / Choe, J. / Zhao, Y. / Lew, J. / Wasney, G. / Alam, Z. / Melone, M. / Kozieradzki, I. / Vedadi, M. ...Dong, A. / Gao, M. / Choe, J. / Zhao, Y. / Lew, J. / Wasney, G. / Alam, Z. / Melone, M. / Kozieradzki, I. / Vedadi, M. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / 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 | 2ghi.cif.gz | 205.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ghi.ent.gz | 163.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ghi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/2ghi ftp://data.pdbj.org/pub/pdb/validation_reports/gh/2ghi | HTTPS FTP |
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-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C 1mv5S 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 29144.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium yoelii yoelii str. 17XNL (eukaryote) Species: Plasmodium yoelii / Strain: yoelii str. 17XNL / Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril / References: UniProt: Q7RBT4 #2: Chemical | ChemComp-SO4 / #3: 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: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 29%Peg 3350, 0.2M Li2SO4, 4% Glycerol, and 0.1M BisTris pH 5.5 , VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 9, 2006 / Details: VariMax HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 56948 / Num. obs: 56948 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.77 / Num. unique all: 2824 / Rsym value: 0.67 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MV5 Resolution: 2.2→32.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.121 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.26 / ESU R Free: 0.241 / 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: 44.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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