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- PDB-5iic: Crystal structure of red abalone VERL repeat 3 at 2.9 A resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iic | |||||||||
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Title | Crystal structure of red abalone VERL repeat 3 at 2.9 A resolution | |||||||||
![]() | Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / Jovine, L. | |||||||||
![]() | ![]() 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 | ![]() | 538.6 KB | Display | ![]() |
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PDB format | ![]() | 453.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ii4C ![]() 5ii5C ![]() 5ii6C ![]() 5ii7C ![]() 5ii8C ![]() 5ii9C ![]() 5iiaC ![]() 5iibC ![]() 5mr2C ![]() 5mr3C ![]() 3setS ![]() 3sexS ![]() 4wrnS 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: Protein | Mass: 54550.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, D4051A, K4052A, E4141A, N4142A, A4184H, K4188H, K4208A, A4281V, I4286V, E4328A, E4331A, D4332A AND R4336N (CORRESPONDING TO A26T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 4340-4453 ARE FROM RED ABALONE VITELLINE ENVELOPE SPERM LYSIN RECEPTOR AND CORRESPOND TO RESIDUES 340-453 OF SWISS-PROT DATABASE ENTRY Q8WR62. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, VERL / Plasmid: pHLsec / Cell line (production host): HEK-293S / Production host: ![]() ![]() #2: Polysaccharide | #3: Sugar | ChemComp-NAG / ![]() ![]() Source method: isolated from a genetically manipulated source Formula: C8H15NO6 Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, D4051A, K4052A, E4141A, N4142A, A4184H, K4188H, K4208A, A4281V, I4286V, E4328A, E4331A, D4332A AND R4336N (CORRESPONDING TO A26T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 4340-4453 ARE FROM RED ABALONE VITELLINE ENVELOPE SPERM LYSIN RECEPTOR AND CORRESPOND TO RESIDUES 340-453 OF SWISS-PROT DATABASE ENTRY Q8WR62. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 4000, 20% isopropanol, 0.1M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→47.805 Å / Num. obs: 22737 / % possible obs: 98 % / Redundancy: 4 % / Biso Wilson estimate: 68.84 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1734 / Net I/σ(I): 7.32 |
Reflection shell | Resolution: 2.9→3.004 Å / Redundancy: 4 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.2 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3SET, 3SEX and 4WRN Resolution: 2.9→47.017 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.08
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.017 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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