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Yorodumi- PDB-2w41: Crystal structure of Plasmodium falciparum glycerol kinase with ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w41 | ||||||
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Title | Crystal structure of Plasmodium falciparum glycerol kinase with ADP | ||||||
Components | GLYCEROL KINASE, PUTATIVE | ||||||
Keywords | TRANSFERASE / CLOSED CONFORMATION / KINASE / MALARIA / PLASMODIUM / SUGAR KINASE/HSP70/ACTIN SUPERFAMILY / GLYCEROL KINASE / OPEN CONFORMATION | ||||||
Function / homology | Function and homology information Triglyceride biosynthesis / glycerol-3-phosphate biosynthetic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / triglyceride metabolic process / phosphorylation / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Schnick, C. / Polley, S.D. / Fivelman, Q.L. / Ranford-Cartwright, L. / Wilkinson, S.R. / Brannigan, J.A. / Wilkinson, A.J. / Baker, D.A. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2009 Title: Structure and Non-Essential Function of Glycerol Kinase in Plasmodium Falciparum Blood Stages. Authors: Schnick, C. / Polley, S.D. / Fivelman, Q.L. / Ranford-Cartwright, L. / Wilkinson, S.R. / Brannigan, J.A. / Wilkinson, A.J. / Baker, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w41.cif.gz | 221.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w41.ent.gz | 175.6 KB | Display | PDB format |
PDBx/mmJSON format | 2w41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/2w41 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/2w41 | HTTPS FTP |
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-Related structure data
Related structure data | 2w40C 1bu6S C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 1 - 501 / Label seq-ID: 7 - 507
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-Components
#1: Protein | Mass: 57335.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: PMAL-C2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IDI4, glycerol kinase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 50MM KFORMATE, 20% PEG 3350, 25% ETHYLENE GLYCOL, 10MM LDAO, 20MM GLYCEROL, THEN SOAKED WITH 5 MM ADP AND 10 MM MGCL2, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→124.03 Å / Num. obs: 39660 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.95 |
Reflection shell | Resolution: 2.41→2.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 0.71 / % possible all: 40.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BU6 Resolution: 2.41→124.03 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.415 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.598 / ESU R Free: 0.301 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→124.03 Å
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Refine LS restraints |
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