+Open data
-Basic information
Entry | Database: PDB / ID: 1z6g | ||||||
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Title | Crystal structure of guanylate kinase from Plasmodium falciparum | ||||||
Components | guanylate kinase | ||||||
Keywords | TRANSFERASE / guanylate kinase / Structural Genomics / SGC / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information : / Interconversion of nucleotide di- and triphosphates / guanylate kinase / guanylate kinase activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Mulichak, A.M. / Lew, J. / Artz, J. / Choe, J. / Walker, J.R. / Zhao, Y. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Mulichak, A.M. / Lew, J. / Artz, J. / Choe, J. / Walker, J.R. / Zhao, Y. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. / Gao, M. / 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 | 1z6g.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z6g.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 1z6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/1z6g ftp://data.pdbj.org/pub/pdb/validation_reports/z6/1z6g | HTTPS FTP |
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-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C 1ex7S 1lvgS 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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-Components
#1: Protein | Mass: 25579.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: custom pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I2M1, guanylate kinase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.4 Details: ammonium sulfate, hepes buffer, pH 7.4, VAPOR DIFFUSION, temperature 298K |
-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: Feb 6, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 14255 / Num. obs: 13877 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.061 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5 % / Num. unique all: 1401 / Rsym value: 0.211 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1EX7 and 1LVG Resolution: 2.18→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.18→30 Å
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