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Open data
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Basic information
Entry | Database: PDB / ID: 2h66 | ||||||
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Title | The Crystal Structure of Plasmodium Vivax 2-Cys peroxiredoxin | ||||||
![]() | PV-PF14_0368 | ||||||
![]() | STRUCTURAL GENOMICS/OXIDOREDUCTASE / plasmodium / vivax / peroxiredoxin / Structural Genomics / Structural Genomics Consortium / SGC / STRUCTURAL GENOMICS-OXIDOREDUCTASE COMPLEX | ||||||
Function / homology | ![]() cellular response to stress / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wernimont, A.K. / Dong, A. / Zhao, Y. / Lew, J. / Melone, M. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. ...Wernimont, A.K. / Dong, A. / Zhao, Y. / Lew, J. / Melone, M. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Artz, J.D. / 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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Remark 999 | SEQUENCE Currently, there is no aminoacid sequence database reference available for the protein |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.1 KB | Display | ![]() |
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PDB format | ![]() | 271.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 509.4 KB | Display | ![]() |
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Full document | ![]() | 546.9 KB | Display | |
Data in XML | ![]() | 60.1 KB | Display | |
Data in CIF | ![]() | 82.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ![]() 2h1rC ![]() 2h2yC ![]() 2hjrC ![]() 2hteC ![]() 2hvgC ![]() 3pggC ![]() 3tb2C ![]() 1qmvS 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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1 |
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Unit cell |
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Details | The biological assembly is a pentagonal ring of dimers, as seen in the asymmetric unit. |
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Components
#1: Protein | Mass: 23732.133 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET28 LIC/TEV DER / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 5% PEG 4000, 50 mM NaAc, 100 mM NaAC, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→41.56 Å / Num. all: 91258 / Num. obs: 86441 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.098 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.48→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5688 / Rsym value: 0.498 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QMV Resolution: 2.5→41.56 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 45.744 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→41.56 Å
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LS refinement shell | Resolution: 2.5→2.565 Å
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