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Yorodumi- PDB-2jix: Crystal structure of ABT-007 FAB fragment with the soluble domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jix | ||||||
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Title | Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor | ||||||
Components |
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Keywords | RECEPTOR/IMMUNE SYSTEM / IMMUNE SYSTEM / RECEPTOR / TRANSMEMBRANE / RECEPTOR SOLUBLE DOMAIN / ANTIBODY / RECEPTOR-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / immunoglobulin complex, circulating / immunoglobulin receptor binding / Erythropoietin activates RAS ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / immunoglobulin complex, circulating / immunoglobulin receptor binding / Erythropoietin activates RAS / complement activation, classical pathway / antigen binding / brain development / cytokine-mediated signaling pathway / heart development / antibacterial humoral response / blood microparticle / nuclear speck / immune response / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Liu, Z. / Stoll, V.S. / DeVries, P. / Jakob, C.G. / Xie, N. / Simmer, R.L. / Lacy, S.E. / Egan, D.A. / Harlan, J.E. / Lesniewski, R.R. / Reilly, E.B. | ||||||
Citation | Journal: Blood / Year: 2007 Title: A Potent Erythropoietin-Mimicking Human Antibody Interacts Through a Novel Binding Site. Authors: Liu, Z. / Stoll, V.S. / Devries, P. / Jakob, C.G. / Xie, N. / Simmer, R.L. / Lacy, S.E. / Egan, D.A. / Harlan, J.E. / Lesniewski, R.R. / Reilly, E.B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jix.cif.gz | 361.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jix.ent.gz | 303.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jix_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 2jix_full_validation.pdf.gz | 510.8 KB | Display | |
Data in XML | 2jix_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 2jix_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jix ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jix | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Unit cell |
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-Components
#1: Antibody | Mass: 23348.893 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7Z3Y4*PLUS #2: Protein | Mass: 24754.000 Da / Num. of mol.: 3 / Fragment: EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P19235 #3: Antibody | Mass: 22946.727 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6GMX6*PLUS |
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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: 3.55 Å3/Da / Density % sol: 65.33 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 50772 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 81.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→113.23 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.822 / SU B: 27.517 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.55 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→113.23 Å
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Refine LS restraints |
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