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- PDB-6e18: Crystal structure of Chlamydomonas reinhardtii HAP2 ectodomain pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6.0E+18 | |||||||||
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Title | Crystal structure of Chlamydomonas reinhardtii HAP2 ectodomain provides structural insights of functional loops in green algae. | |||||||||
![]() | Hapless 2 | |||||||||
![]() | MEMBRANE PROTEIN / Gamete fusion / membrane binding motif / glycoprotein / cystine ladder | |||||||||
Function / homology | ![]() fusion of sperm to egg plasma membrane involved in single fertilization / cell projection membrane / protein insertion into membrane / cytoplasmic vesicle membrane / cytoplasmic vesicle / lipid binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Baquero, E. / Legrand, P. / Rey, F.A. | |||||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Species-Specific Functional Regions of the Green Alga Gamete Fusion Protein HAP2 Revealed by Structural Studies. Authors: Baquero, E. / Fedry, J. / Legrand, P. / Krey, T. / Rey, F.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.9 KB | Display | ![]() |
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PDB format | ![]() | 177.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mf1S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61432.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar |
-Non-polymers , 2 types, 84 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.91 Å3/Da / Density % sol: 80 % / Description: Small hexagonal plates Preparation: The sample used for crystallization was a complex of Chlamydomonas reinhardtii HAP2 ectodomain with an antibody fragment scFv. However we could not reveal the presence of the scFv in our ...Preparation: The sample used for crystallization was a complex of Chlamydomonas reinhardtii HAP2 ectodomain with an antibody fragment scFv. However we could not reveal the presence of the scFv in our electron density maps. There are two possible explanations: 1) The bound scFv was displaced due to crystallization conditions/packing or 2) The scFv is still bound but disordered because is interacting with one of the disordered loops located in the large solvent volumes between the protomers. In this last case, it is expected that the solvent content of the crystal would be lower than the one currently reported |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M LiSO4, 0.1M Tris-HCl pH 8.5 and 25% w/v PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.6→40.13 Å / Num. obs: 53971 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 67.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0592 / Rpim(I) all: 0.091 / Rrim(I) all: 0.406 / Net I/σ(I): 8.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MF1 Resolution: 2.6→38.99 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.281 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.227 Details: Due to marked diffraction anisotropy we post-processed the scaled intensities with the STARANISO program that performs an ellipsoidal resolution cut-off. The classical completeness is 70% up ...Details: Due to marked diffraction anisotropy we post-processed the scaled intensities with the STARANISO program that performs an ellipsoidal resolution cut-off. The classical completeness is 70% up to 2.6A resolution, but the "ellipsoidal completeness" is 94.5% up to the same resolution (79% in the last ellipsoidal shell).
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Displacement parameters | Biso max: 136.28 Å2 / Biso mean: 50.89 Å2 / Biso min: 21.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→38.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Origin x: -51.3026 Å / Origin y: 26.2073 Å / Origin z: -25.4354 Å
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Refinement TLS group |
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