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- PDB-4jam: Crystal structure of broadly neutralizing anti-hiv-1 antibody ch103 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jam | ||||||
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Title | Crystal structure of broadly neutralizing anti-hiv-1 antibody ch103 | ||||||
![]() | (ANTIGEN BINDING FRAGMENT OF ...) x 2 | ||||||
![]() | IMMUNE SYSTEM / NEUTRALIZATION / VACCINE / HIV-1 / Antibody / immunoglobulin | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, T. / Moquin, S. / Zheng, A. / Srivatsan, S. / Kwong, P.D. | ||||||
![]() | ![]() Title: Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / ...Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / Hraber, P. / Wiehe, K. / Kelsoe, G. / Yang, G. / Xia, S.M. / Montefiori, D.C. / Parks, R. / Lloyd, K.E. / Scearce, R.M. / Soderberg, K.A. / Cohen, M. / Kamanga, G. / Louder, M.K. / Tran, L.M. / Chen, Y. / Cai, F. / Chen, S. / Moquin, S. / Du, X. / Joyce, M.G. / Srivatsan, S. / Zhang, B. / Zheng, A. / Shaw, G.M. / Hahn, B.H. / Kepler, T.B. / Korber, B.T. / Kwong, P.D. / Mascola, J.R. / Haynes, B.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 489 KB | Display | ![]() |
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PDB format | ![]() | 410.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.9 KB | Display | ![]() |
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Full document | ![]() | 509.6 KB | Display | |
Data in XML | ![]() | 41.5 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4janC ![]() 3se9S 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
-Antibody , 2 types, 4 molecules HALB
#1: Antibody | Mass: 23896.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 22533.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 4 types, 755 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 170 mM ammonium sulfate, 25.5 % PEG 4000, 15% Glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2012 / Details: APS 22ID |
Radiation | Monochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 97300 / Num. obs: 95840 / % possible obs: 98.4 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.067 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.53 / % possible all: 90.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SE9 Resolution: 1.65→38.185 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 20.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→38.185 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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