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Yorodumi- PDB-2ymo: Crystal structure of Pf12 tandem 6-cys domains from Plasmodium fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ymo | ||||||
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Title | Crystal structure of Pf12 tandem 6-cys domains from Plasmodium falciparum | ||||||
Components | PF12 | ||||||
Keywords | MEMBRANE PROTEIN / APICOMPLEXA / MALARIA / 6-CYSTEINE / BLOOD STAGE ANTIGEN / VACCINE | ||||||
Function / homology | Function and homology information symbiont-containing vacuolar space / symbiont entry into host / side of membrane / apical part of cell / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tonkin, M.L. / Arredondo, S.A. / Loveless, B.C. / Grigg, M.E. / Miller, L.H. / Boulanger, M.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural and Biochemical Characterization of Plasmodium Falciparum 12 (Pf12) Reveals a Unique Inter-Domain Organization and the Potential for an Antiparallel Arrangement with Pf41 Authors: Tonkin, M.L. / Arredondo, S.A. / Loveless, B.C. / Serpa, J.J. / Makepeace, K.A.T. / Sundar, N. / Petrotchenko, E.V. / Miller, L.H. / Grigg, M.E. / Boulanger, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ymo.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ymo.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ymo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/2ymo ftp://data.pdbj.org/pub/pdb/validation_reports/ym/2ymo | HTTPS FTP |
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-Related structure data
Related structure data | 2loeS 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: 32610.357 Da / Num. of mol.: 1 / Fragment: TANDEM S48/45 DOMAINS, RESIDUES 28-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: PACGP67B / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: C6KSX0 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.1 % / Description: NONE |
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Crystal grow | Details: 20 MM CALCIUM CHLORIDE DIHYDRATE, 20 MM CADMIUM CHLORIDE HYDRATE, 20 MM COBALT CHLORIDE HEXAHYDRATE AND 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.52 Å / Num. obs: 22181 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2LOE Resolution: 1.9→42.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.399 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.165 / 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: 41.092 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.5 Å
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