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Yorodumi- PDB-4qxt: Crystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qxt | ||||||
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Title | Crystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex with FC27-MSP2 14-30 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin fold / N-TERMINAL MSP2 / unstructured antigen | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Plasmodium falciparum K1 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Morales, R.A.V. / MacRaild, C.A. / Seow, J. / Bankala, K. / Drinkwater, N. / McGowan, S. / Rouet, R. / Christ, D. / Anders, R.F. / Norton, R.S. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structural basis for epitope masking and strain specificity of a conserved epitope in an intrinsically disordered malaria vaccine candidate. Authors: Morales, R.A. / MacRaild, C.A. / Seow, J. / Krishnarjuna, B. / Drinkwater, N. / Rouet, R. / Anders, R.F. / Christ, D. / McGowan, S. / Norton, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qxt.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qxt.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qxt ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qxt | HTTPS FTP |
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-Related structure data
Related structure data | 4qy8C 4qyoSC 4r3sC 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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-Components
#1: Antibody | Mass: 12489.899 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 11959.071 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Protein/peptide | Mass: 1941.137 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-49 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum K1 (eukaryote) / References: UniProt: Q03643 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 30% PEG 8000, 0.2M NaCl, 0.1M NaOAc, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→34.4 Å / Num. all: 28478 / Num. obs: 28505 / % possible obs: 99.9 % |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 6.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QYO Resolution: 1.58→34.388 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 18.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→34.388 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.1739 Å / Origin y: -12.609 Å / Origin z: -12.2338 Å
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Refinement TLS group | Selection details: ALL |