+Open data
-Basic information
Entry | Database: PDB / ID: 3h3p | ||||||
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Title | Crystal structure of HIV epitope-scaffold 4E10 Fv complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / epitope-scaffold Fv complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) artificial gene (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Holmes, M.A. | ||||||
Citation | Journal: J.Virol. / Year: 2010 Title: Interactions between lipids and human anti-HIV antibody 4E10 can be reduced without ablating neutralizing activity Authors: Xu, H. / Song, L. / Kim, M. / Holmes, M.A. / Kraft, Z. / Sellhorn, G. / Reinherz, E.L. / Stamatatos, L. / Strong, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h3p.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h3p.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h3p_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
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Full document | 3h3p_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 3h3p_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3h3p_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/3h3p ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h3p | HTTPS FTP |
-Related structure data
Related structure data | 1tzgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 14712.454 Da / Num. of mol.: 2 / Mutation: W104A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL #2: Antibody | Mass: 12304.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL #3: Protein | Mass: 10501.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The author states that THE EPITOPE-SCAFFOLD IS BASED on transcription factor DksA from E. coli (PDB ID 1TJL). Source: (gene. exp.) artificial gene (others) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Sequence details | FV HEAVY CHAIN CONTAINS A REMNANT OF SINGLE-CHAIN LINKER AT N-TERMINUS GS. FV LIGHT CHAIN CONTAINS ...FV HEAVY CHAIN CONTAINS A REMNANT OF SINGLE-CHAIN LINKER AT N-TERMINUS GS. FV LIGHT CHAIN CONTAINS A REMNANT OF SINGLE-CHAIN LINKER AT C-TERMINUS KLVPR. FV HEAVY CHAIN HAS BEEN MUTATED TO ALA AT POSITION 104 (KABAT POSITION 100) | |
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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: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M calcium acetate, 8% PEG 8000, 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 107 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 13, 2008 / Details: Rigaku VariMax HR |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→69.02 Å / Num. all: 19557 / Num. obs: 19557 / % possible obs: 98.6 % / Redundancy: 4.56 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8305 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: computationally-derived model of the Fv, based on 1TZG Resolution: 2.7→60.08 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / SU B: 25.371 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, 1 tls group per chain / Cross valid method: THROUGHOUT / ESU R: 0.725 / ESU R Free: 0.364 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→60.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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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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