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Open data
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Basic information
Entry | Database: PDB / ID: 5cip | |||||||||
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Title | Crystal Structure of Unbound 4E10 | |||||||||
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![]() | IMMUNE SYSTEM / BROADLY NEUTRALIZING ANTIBODY / RECOMBINANT FAB / ENV-PEPTIDE / HIV-1 / EPITOPE | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Caaveiro, J.M.M. / Rujas, E. / Nieva, J.L. / Tsumoto, K. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10 Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.3 KB | Display | ![]() |
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PDB format | ![]() | 138.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.5 KB | Display | ![]() |
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Full document | ![]() | 449.5 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cilC ![]() 5cinC ![]() 4wy7S 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: Antibody | Mass: 23861.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Antibody | Mass: 23106.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | | Mass: 23732.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.68 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM MES, 15% PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.48→44.7 Å / Num. obs: 32268 / % possible obs: 98.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.7 | |||||||||||||||
Reflection shell | Resolution: 2.48→2.61 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.2 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WY7 Resolution: 2.48→42.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.434 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS. FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.276 Å2
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Refinement step | Cycle: 1 / Resolution: 2.48→42.97 Å
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Refine LS restraints |
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