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- PDB-6pyq: Assembly of VIQKI D455(beta-L-homoaspartic acid)with human parain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pyq | |||||||||
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Title | Assembly of VIQKI D455(beta-L-homoaspartic acid)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain | |||||||||
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![]() | VIRAL PROTEIN / Fusion glycoprotein / six-helix bundle / foldamer | |||||||||
Function / homology | ![]() symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Outlaw, V.K. / Gellman, S.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Effects of Single alpha-to-beta Residue Replacements on Recognition of an Extended Segment in a Viral Fusion Protein. Authors: Outlaw, V.K. / Kreitler, D.F. / Stelitano, D. / Porotto, M. / Moscona, A. / Gellman, S.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.7 KB | Display | ![]() |
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PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6prlC ![]() 6pz6C ![]() 6v3vC ![]() 6vasC ![]() 6nroS S: Starting model for refinement C: citing same article ( |
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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: 5656.473 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Protein/peptide | Mass: 4208.921 Da / Num. of mol.: 3 Mutation: D455(beta-L-homoaspartic acid), E459V, A463I, D466Q, Q479K, K480I Source method: obtained synthetically Source: (synth.) ![]() References: UniProt: P06828 #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM imidazole/MES monohydrate (pH 6.5), 12.5% PEG1000, 12.5% PEG3350, 12.5% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→24.73 Å / Num. obs: 20102 / % possible obs: 99.76 % / Redundancy: 8.5 % / Biso Wilson estimate: 29.85 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.031 / Rrim(I) all: 0.089 / Rsym value: 0.084 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.79→1.82 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1037 / CC1/2: 0.395 / Rpim(I) all: 0.732 / Rrim(I) all: 2.151 / Rsym value: 2.021 / % possible all: 99.71 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NRO Resolution: 1.79→24.73 Å / SU ML: 0.1929 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6996
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→24.73 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.0066805196 Å / Origin y: 4.74655574207 Å / Origin z: 18.1354917334 Å
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Refinement TLS group | Selection details: all |