+Open data
-Basic information
Entry | Database: PDB / ID: 6cxg | |||||||||
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Title | anti-HIV-1 Fab 2G12 in complex with glycopeptide 10V1S | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / glycopeptide / HIV-1 / glycobiology | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å | |||||||||
Authors | Stanfield, R.L. / Wilson, I.A. | |||||||||
Citation | Journal: ACS Cent Sci / Year: 2019 Title: Oligomannose Glycopeptide Conjugates Elicit Antibodies Targeting the Glycan Core Rather than Its Extremities. Authors: Nguyen, D.N. / Xu, B. / Stanfield, R.L. / Bailey, J.K. / Horiya, S. / Temme, J.S. / Leon, D.R. / LaBranche, C.C. / Montefiori, D.C. / Costello, C.E. / Wilson, I.A. / Krauss, I.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cxg.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cxg.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 6cxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/6cxg ftp://data.pdbj.org/pub/pdb/validation_reports/cx/6cxg | HTTPS FTP |
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-Related structure data
Related structure data | 6cxlC 4rbpS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein/peptide , 1 types, 2 molecules AC
#3: Protein/peptide | Mass: 5042.738 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Antibody , 2 types, 4 molecules LKHM
#1: Antibody | Mass: 23201.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293freestyle / Production host: Homo sapiens (human) #2: Antibody | Mass: 23845.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293freestyle / Production host: Homo sapiens (human) |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 426 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1M citrate, 10mM sodium borate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.298→42.4 Å / Num. obs: 45804 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.095 / Rrim(I) all: 0.193 / Rsym value: 0.174 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.298→2.34 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2195 / CC1/2: 0.51 / Rpim(I) all: 0.506 / Rrim(I) all: 1 / Rsym value: 1 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RBP Resolution: 2.298→42.385 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.298→42.385 Å
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Refine LS restraints |
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LS refinement shell |
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