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Yorodumi- PDB-3c02: X-ray structure of the aquaglyceroporin from Plasmodium falciparum -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c02 | ||||||
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Title | X-ray structure of the aquaglyceroporin from Plasmodium falciparum | ||||||
Components | Aquaglyceroporin | ||||||
Keywords | MEMBRANE PROTEIN / glycerol / water / transport / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Porin / Transmembrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Newby, Z.E. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum. Authors: Newby, Z.E. / O'Connell, J. / Robles-Colmenares, Y. / Khademi, S. / Miercke, L.J. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c02.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c02.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 3c02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c02_validation.pdf.gz | 609.3 KB | Display | wwPDB validaton report |
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Full document | 3c02_full_validation.pdf.gz | 613.3 KB | Display | |
Data in XML | 3c02_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3c02_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/3c02 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/3c02 | HTTPS FTP |
-Related structure data
Related structure data | 1fx8S 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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-Components
#1: Protein | Mass: 28319.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: AQP / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8WPZ6 | ||
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#2: Sugar | ChemComp-BOG / | ||
#3: Chemical | ChemComp-GOL / #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: 3.64 Å3/Da / Density % sol: 66.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 17% PEG MME 2000, 0.1M Sodium citrate, 15% Glycerol, 0.04M n-octyl-B-D-glucopyranoside, 0.01 Nickel sulfate, 0.01M DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2007 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→46.2 Å / Num. all: 25478 / Num. obs: 24719 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.06 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.25 / Num. unique all: 1819 / Rsym value: 0.435 / % possible all: 69.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FX8 Resolution: 2.05→46.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.214 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.134 / ESU R Free: 0.12 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.452 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→46.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.11 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 8.552 Å / Origin y: 19.124 Å / Origin z: 22.738 Å
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