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Open data
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Basic information
Entry | Database: PDB / ID: 2a4a | ||||||
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Title | Deoxyribose-phosphate aldolase from P. yoelii | ||||||
![]() | deoxyribose-phosphate aldolase | ||||||
![]() | LYASE / ALDOLASE / TIM BETA/ALPHA BARREL / DEOC / DERA / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walker, J.R. / Amani, M. / Lew, J. / Wiegelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. / Vedadi, M. / 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113 KB | Display | ![]() |
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PDB format | ![]() | 87.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1txjC ![]() 1xccC ![]() 1y6zC ![]() 1z6gC ![]() 1z7dC ![]() 1z81C ![]() 1zo2C ![]() 2a22C ![]() 2aifC ![]() 2amxC ![]() 2aqwC ![]() 2av4C ![]() 2awpC ![]() 2ayvC ![]() 2b71C ![]() 2bddC ![]() 2f4zC ![]() 2fdsC ![]() 2ffcC ![]() 2fo3C ![]() 2fu0C ![]() 2ghiC ![]() 2h1rC ![]() 2h2yC ![]() 2h66C ![]() 2hjrC ![]() 2hteC ![]() 2hvgC ![]() 3pggC ![]() 3tb2C ![]() 1jclS 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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Unit cell |
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Details | The biological unit is a monomer. |
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Components
#1: Protein | Mass: 31264.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 42.83 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: PEG4K, Tris pH 8.5, NaCl 0.2 M, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→34.68 Å / Num. obs: 41400 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.56 / % possible all: 87.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JCL Resolution: 1.84→34.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.079 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.151 / 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: 33.875 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→34.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.837→1.885 Å / Total num. of bins used: 20
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