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- PDB-4qyo: Crystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qyo | ||||||
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Title | Crystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex with MSP2 14-22 | ||||||
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![]() | IMMUNE SYSTEM / Immunoglobulin fold / N-TERMINAL MSP2 / unstructured antigen | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.2 KB | Display | ![]() |
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PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qxtC ![]() 4qy8C ![]() 4r3sC ![]() 3gm0S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1150.337 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-41 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 22% PEG 8000, 0.2M NaCl, 0.1M NaOAc, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 29, 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: 1.208→41.864 Å / Num. all: 62158 / Num. obs: 62158 / % possible obs: 96.75 % |
Reflection shell | Resolution: 1.208→1.251 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 5342 / % possible all: 83.25 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 3GM0 Resolution: 1.208→41.864 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 17.6 / Stereochemistry target values: Engh & Huber
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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: 1.208→41.864 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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Refinement TLS params. | Method: refined / Origin x: 19.8775 Å / Origin y: 17.242 Å / Origin z: 33.177 Å
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Refinement TLS group | Selection details: ALL |