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- PDB-3o3x: Crystal structure of gp41-5, a single-chain 5-helix-bundle based ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o3x | ||||||
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Title | Crystal structure of gp41-5, a single-chain 5-helix-bundle based on HIV gp41 | ||||||
![]() | gp41-5 | ||||||
![]() | VIRAL PROTEIN / helix bundle / mimic of HIV gp41 | ||||||
Function / homology | ISOPROPYL ALCOHOL![]() | ||||||
Biological species | artificial gene (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horne, W.S. / Johnson, L.M. / Gellman, S.H. | ||||||
![]() | ![]() Title: Broad Distribution of Energetically Important Contacts across an Extended Protein Interface. Authors: Johnson, L.M. / Horne, W.S. / 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 | ![]() | 169 KB | Display | ![]() |
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PDB format | ![]() | 135.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.3 KB | Display | ![]() |
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Full document | ![]() | 458.4 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3o3zC ![]() 3o40C ![]() 3o43C ![]() 1aikS 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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Unit cell |
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Components
#1: Protein | Mass: 22246.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MPD / ( |
#3: Chemical | ChemComp-IPA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 20% v/v iPrOH, 20% w/v PEG 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2008 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 34965 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rsym value: 0.097 / Net I/σ(I): 21.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5-helix-bundle derived from PDB entry 1AIK Resolution: 1.45→25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.965 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.144 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.452→1.49 Å / Total num. of bins used: 20
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