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Yorodumi- PDB-5ow4: Crystal structure of a protease-resistant fragment of the Trypano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ow4 | ||||||
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Title | Crystal structure of a protease-resistant fragment of the Trypanosoma cruzi gamete fusion protein HAP2 ectodomain | ||||||
Components | Uncharacterized protein | ||||||
Keywords | MEMBRANE PROTEIN / Gamete fusion protein / class II fold / HAP2 / Membrane fusion | ||||||
Function / homology | Generative cell specific-1/HAP2 domain / Male gamete fusion factor / HAP2/GCS1 / single fertilization / membrane => GO:0016020 / plasma membrane / HAP2-GCS1 domain-containing protein Function and homology information | ||||||
Biological species | Trypanosoma cruzi strain CL Brener (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Fedry, J. / Rey, F.A. / Krey, T. | ||||||
Funding support | France, 1items
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Citation | Journal: PLoS Biol. / Year: 2018 Title: Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes. Authors: Fedry, J. / Forcina, J. / Legrand, P. / Pehau-Arnaudet, G. / Haouz, A. / Johnson, M. / Rey, F.A. / Krey, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ow4.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ow4.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ow4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ow4_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 5ow4_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 5ow4_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5ow4_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/5ow4 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/5ow4 | HTTPS FTP |
-Related structure data
Related structure data | 5ow3C 5mf1S S: Starting model for refinement C: citing same article (ref.) |
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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: 64553.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote) Gene: Tc00.1047053509105.4 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q4DKJ2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100mM CHES pH9.0 200mM NaCl 10%w/v PEG 8K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 15453 / % possible obs: 97.7 % / Redundancy: 8.9 % / Biso Wilson estimate: 116.25 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.201 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2389 / CC1/2: 0.41 / Rrim(I) all: 2.493 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MF1 Resolution: 3.1→49.13 Å / Cor.coef. Fo:Fc: 0.8853 / Cor.coef. Fo:Fc free: 0.8521 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.349 / SU Rfree Blow DPI: 0.277 / SU Rfree Cruickshank DPI: 0.278
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Displacement parameters | Biso mean: 84.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.659 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.1→49.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.31 Å / Total num. of bins used: 8
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