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Open data
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Basic information
Entry | Database: PDB / ID: 7uny | |||||||||
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Title | Crystal structure of D2 nanobody in complex with PfCSS | |||||||||
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![]() | CELL INVASION / 6-Cys protein / nanobody | |||||||||
Function / homology | Cysteine-rich small secreted protein CSS, putative![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Scally, S.W. / Lim, P.S. / Cowman, A.F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum. Authors: Scally, S.W. / Triglia, T. / Evelyn, C. / Seager, B.A. / Pasternak, M. / Lim, P.S. / Healer, J. / Geoghegan, N.D. / Adair, A. / Tham, W.H. / Dagley, L.F. / Rogers, K.L. / Cowman, A.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.4 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7unzC ![]() 6waqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33384.188 Da / Num. of mol.: 2 / Mutation: T263A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: PF3D7_1404700 / Production host: ![]() ![]() #2: Antibody | Mass: 14171.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6 M ammonium sulfate, 0.1 M sodium chloride, 0.1 M sodium HEPES pH 7.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 4.13→39.49 Å / Num. obs: 21543 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 161.93 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.071 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 4.13→4.46 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4391 / CC1/2: 0.615 / Rpim(I) all: 0.485 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WAQ Resolution: 4.13→39.49 Å / SU ML: 0.5779 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.202 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 202.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.13→39.49 Å
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Refine LS restraints |
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LS refinement shell |
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