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Yorodumi- PDB-1rzi: Crystal structure of human anti-HIV-1 gp120-reactive antibody 47e fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rzi | ||||||
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Title | Crystal structure of human anti-HIV-1 gp120-reactive antibody 47e fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / gp120 / CD4i / antibodies / tyrosine sulfation / VH-gene usage | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. ...Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120 Authors: Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rzi.cif.gz | 631.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rzi.ent.gz | 538.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzi ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzi | HTTPS FTP |
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-Related structure data
Related structure data | 1rz7C 1rz8C 1rzfC 1rzgC 1rzjC 1rzkC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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8 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23166.619 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Human herpesvirus 4 (Epstein-Barr virus) #2: Antibody | Mass: 24157.945 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Human herpesvirus 4 (Epstein-Barr virus) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.2M ammonium citrate, 0.1M Tris-HCl, 4% PEG1000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003 |
Radiation | Monochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 84392 / Observed criterion σ(I): -3 / Biso Wilson estimate: 64.3 Å2 |
Reflection shell | Resolution: 2.8→2.91 Å / % possible all: 31.1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % possible obs: 81.9 % / Num. measured all: 390048 / Rmerge(I) obs: 0.176 |
Reflection shell | *PLUS % possible obs: 31.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 257118.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.3048 Å2 / ksol: 0.267058 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.319 / Rfactor Rwork: 0.231 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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