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- PDB-5mr2: Crystal structure of red abalone VERL repeat 2 with linker at 2.5... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mr2 | |||||||||||||||||||||
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Title | Crystal structure of red abalone VERL repeat 2 with linker at 2.5 A resolution | |||||||||||||||||||||
![]() | Vitelline envelope sperm lysin receptor | |||||||||||||||||||||
![]() | CELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / VITELLINE ENVELOPE / SPERM RECEPTOR | |||||||||||||||||||||
Function / homology | vitelline envelope / Vitelline envelope, lysin receptor / Vitelline envelope receptor for lysin / sperm-egg recognition / ZP domain profile. / Zona pellucida domain / extracellular region / plasma membrane / Vitelline envelope sperm lysin receptor![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Sadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / De Sanctis, D. / Jovine, L. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Egg Coat-Sperm Recognition at Fertilization. Authors: Raj, I. / Sadat Al Hosseini, H. / Dioguardi, E. / Nishimura, K. / Han, L. / Villa, A. / de Sanctis, D. / Jovine, L. #1: Journal: Mol. Biol. Evol. / Year: 2011 Title: The molecular basis of sex: linking yeast to human. Authors: Swanson, W.J. / Aagaard, J.E. / Vacquier, V.D. / Monne, M. / Sadat Al Hosseini, H. / Jovine, L. #2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2006 Title: Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs. Authors: Aagaard, J.E. / Yi, X. / MacCoss, M.J. / Swanson, W.J. #3: Journal: Gene / Year: 2002 Title: Full-length sequence of VERL, the egg vitelline envelope receptor for abalone sperm lysin. Authors: Galindo, B.E. / Moy, G.W. / Swanson, W.J. / Vacquier, V.D. #4: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1997 Title: The abalone egg vitelline envelope receptor for sperm lysin is a giant multivalent molecule. Authors: Swanson, W.J. / Vacquier, V.D. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.1 KB | Display | ![]() |
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PDB format | ![]() | 161.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.7 KB | Display | ![]() |
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Full document | ![]() | 481.3 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ii4C ![]() 5ii5C ![]() 5ii6C ![]() 5ii7C ![]() 5ii8C ![]() 5ii9C ![]() 5iiaSC ![]() 5iibSC ![]() 5iicSC ![]() 5mr3C 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15089.334 Da / Num. of mol.: 3 / Fragment: UNP residues 176-298 / Mutation: S293A, S296A, S297A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ![]() Source method: isolated from a genetically manipulated source Formula: C8H15NO6 / Source: (gene. exp.) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.2 M ammonium formate pH 6.6, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.01 Å / Num. obs: 15039 / % possible obs: 100 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1382 / Net I/σ(I): 7.79 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 4.4 % / Rmerge(I) obs: 2.386 / Mean I/σ(I) obs: 0.62 / CC1/2: 0.222 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IIA, 5IIB, 5IIC Resolution: 2.5→47.006 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.006 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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