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- PDB-2h1r: Crystal structure of a dimethyladenosine transferase from Plasmod... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h1r | ||||||
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Title | Crystal structure of a dimethyladenosine transferase from Plasmodium falciparum | ||||||
![]() | Dimethyladenosine transferase, putative | ||||||
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Function / homology | ![]() Mitochondrial transcription initiation / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methyltransferase activity / rRNA methylation / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, A. / Lew, J. / Ren, H. / Sundararajan, E. / Zhao, Y. / Wasney, G. / Vedadi, M. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Lew, J. / Ren, H. / Sundararajan, E. / Zhao, Y. / Wasney, G. / Vedadi, M. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Qiu, W. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.6 KB | Display | ![]() |
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PDB format | ![]() | 101.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ![]() 2ghiC ![]() 2h2yC ![]() 2h66C ![]() 2hjrC ![]() 2hteC ![]() 2hvgC ![]() 3pggC ![]() 3tb2C ![]() 1zq9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34639.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow![]() | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 23.5% PEG3350, 0.2M Tri Lithium Citrate, 0.1M Hepes at pH7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 7, 2006 / Details: Si(111) |
Radiation | Monochromator: Si(111) monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→50 Å / Num. all: 55385 / Num. obs: 55385 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.95 / Rsym value: 0.474 / % possible all: 87.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1ZQ9 Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.467 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.148 / 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: 29.872 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.892→1.941 Å / Total num. of bins used: 20
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