+Open data
-Basic information
Entry | Database: PDB / ID: 2h66 | ||||||
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Title | The Crystal Structure of Plasmodium Vivax 2-Cys peroxiredoxin | ||||||
Components | PV-PF14_0368 | ||||||
Keywords | STRUCTURAL GENOMICS/OXIDOREDUCTASE / plasmodium / vivax / peroxiredoxin / Structural Genomics / Structural Genomics Consortium / SGC / STRUCTURAL GENOMICS-OXIDOREDUCTASE COMPLEX | ||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | 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) | ||||||
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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Remark 999 | SEQUENCE Currently, there is no aminoacid sequence database reference available for the protein |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h66.cif.gz | 333.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h66.ent.gz | 271.3 KB | Display | PDB format |
PDBx/mmJSON format | 2h66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h66_validation.pdf.gz | 509.4 KB | Display | wwPDB validaton report |
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Full document | 2h66_full_validation.pdf.gz | 546.9 KB | Display | |
Data in XML | 2h66_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 2h66_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h66 ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h66 | 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 (ref.) |
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Similar structure data |
-Links
-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. |
-Components
#1: Protein | Mass: 23732.133 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Plasmid: pET28 LIC/TEV DER / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus/RIL / References: UniProt: A5K421 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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