+Open data
-Basic information
Entry | Database: PDB / ID: 6y3a | ||||||
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Title | Structure of Plasmodium vivax phosphoglycerate kinase | ||||||
Components | Phosphoglycerate kinase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / phosphoglycerate kinase / metabolic enzyme / kinase | ||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Blaszczyk, B.K. / Hyvonen, M. | ||||||
Citation | Journal: to be published Title: Phosphoglycerate Kinase as a potential target for antimalarial therapy Authors: Bilsland, E. / Costa, F. / Blaszczyk, B.K. / Hyvonen, M. / Sunnerhagen, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y3a.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y3a.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 6y3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y3a_validation.pdf.gz | 420 KB | Display | wwPDB validaton report |
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Full document | 6y3a_full_validation.pdf.gz | 420.7 KB | Display | |
Data in XML | 6y3a_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6y3a_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/6y3a ftp://data.pdbj.org/pub/pdb/validation_reports/y3/6y3a | HTTPS FTP |
-Related structure data
Related structure data | 6yjeC 6yjfC 1ltkS 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: 46246.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVX_099535 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5K6T9, phosphoglycerate kinase |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-BR / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.4 / Details: 20% PEG-MME 2K, 0.15 M KBr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 20, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92818 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.49→69.88 Å / Num. obs: 74103 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 14 / Num. measured all: 428316 / Scaling rejects: 5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ltk Resolution: 1.49→69.879 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.68 Å2 / Biso mean: 27.4428 Å2 / Biso min: 11.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→69.879 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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