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Yorodumi- PDB-8vtr: Structure of FabS1CE3-EPR-1, an elbow-locked high affinity antibo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vtr | |||||||||
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Title | Structure of FabS1CE3-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor (orthorhombic form) | |||||||||
Components | (S1CE3 VARIANT OF FAB-EPR-1 ...) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization | |||||||||
Function / homology | CITRIC ACID / DI(HYDROXYETHYL)ETHER Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | |||||||||
Authors | Singer, A.U. / Bruce, H.A. / Pavlenco, A. / Ploder, L. / Luu, G. / Blazer, L. / Adams, J.J. / Sidhu, S.S. | |||||||||
Funding support | Canada, United States, 2items
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Citation | Journal: Protein Sci. / Year: 2024 Title: Antigen-binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones. Authors: Bruce, H.A. / Singer, A.U. / Blazer, L.L. / Luu, K. / Ploder, L. / Pavlenco, A. / Kurinov, I. / Adams, J.J. / 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 | 8vtr.cif.gz | 204.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vtr.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vtr_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
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Full document | 8vtr_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 8vtr_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 8vtr_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/8vtr ftp://data.pdbj.org/pub/pdb/validation_reports/vt/8vtr | HTTPS FTP |
-Related structure data
Related structure data | 8vtpC 8vu1C 8vu4C 8vuaC 8vucC 8vuiC 8vvmC 8vvoC 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 , 2 types, 2 molecules AG
#1: Antibody | Mass: 24135.057 Da / Num. of mol.: 1 / Mutation: F160W Source method: isolated from a genetically manipulated source Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 COMP IMMUNOL. 2003 JAN;27(1):55-77) NUMBERING Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23049.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 COMP IMMUNOL. 2003 JAN;27(1):55-77) NUMBERING Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
-Non-polymers , 5 types, 263 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CIT / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | This is an open structure which forms a linear polymeric array |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium Citrate dibasic, 20% PEG3350. This was set up as a Fab/EPOR complex, however no EPOR was observed upon solving the structure. |
-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 EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→74.28 Å / Num. obs: 37275 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 6 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2602 / CC1/2: 0.855 / Rpim(I) all: 0.302 / Rsym value: 0.751 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→58.12 Å / SU ML: 0.2192 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4191 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→58.12 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 | Refine-ID: X-RAY DIFFRACTION
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