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Yorodumi- PDB-8t8i: Structure of VHH-Fab complex with engineered Elbow FNQIKG, Crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t8i | ||||||
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Title | Structure of VHH-Fab complex with engineered Elbow FNQIKG, Crystal Kappa and SER substitutions | ||||||
Components |
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Keywords | IMMUNE SYSTEM / NabFab / Nanobody / Antibody Fragment | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / SUCCINIC ACID Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Filippova, E.V. / Thompson, I. / Kossiakoff, A.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / Atwell, S. / Kossiakoff, A.A. / Sidhu, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t8i.cif.gz | 237.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t8i.ent.gz | 190.8 KB | Display | PDB format |
PDBx/mmJSON format | 8t8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/8t8i ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t8i | HTTPS FTP |
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-Related structure data
Related structure data | 8t58C 8t6iC 8t7fC 8t7gC 8t7iC 8t9yC 8trsC 8trtC 8ts5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 3 types, 3 molecules ALH
#1: Antibody | Mass: 14170.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET26B+ / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Antibody | Mass: 23018.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: "QGTTS" - Crystal Kappa substitution "Q149S" and "K150Y" - SER substitution Source: (gene. exp.) Homo sapiens (human) / Plasmid: RH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 |
#3: Antibody | Mass: 25753.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: "FNQIKG" - elbow region substitution / Source: (gene. exp.) Homo sapiens (human) / Plasmid: RH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 |
-Non-polymers , 5 types, 76 molecules
#4: Chemical | ChemComp-SIN / | ||||
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#5: Chemical | ChemComp-PEG / | ||||
#6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.72 Å3/Da / Density % sol: 66.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2% Tacsimate pH 5.0, 0.1 M Na citrate tribasic dihydrate, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→121.2 Å / Num. obs: 32276 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.52→2.62 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3603 / CC1/2: 0.37 / Rpim(I) all: 0.78 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→121.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 26.907 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 83.249 Å2
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Refinement step | Cycle: 1 / Resolution: 2.52→121.2 Å
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Refine LS restraints |
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