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- PDB-1wej: IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wej | ||||||
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Title | IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION | ||||||
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![]() | COMPLEX (ANTIBODY/ELECTRON TRANSPORT) / IMMUNOGLOBULIN / IGG1 KAPPA / FAB FRAGMENT / HORSE CYTOCHROME C / COMPLEX (ANTIBODY-ELECTRON TRANSPORT) / COMPLEX (ANTIBODY-ELECTRON TRANSPORT) complex | ||||||
Function / homology | ![]() cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / immunoglobulin complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / adaptive immune response ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / immunoglobulin complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / adaptive immune response / electron transfer activity / immune response / positive regulation of apoptotic process / lipid binding / heme binding / apoptotic process / extracellular space / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mylvaganam, S.E. / Paterson, Y. / Getzoff, E.D. | ||||||
![]() | ![]() Title: Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution. Authors: Mylvaganam, S.E. / Paterson, Y. / Getzoff, E.D. #1: ![]() Title: Biochemical Implications from the Variable Gene Sequences of an Anti-Cytochrome C Antibody and Crystallographic Characterization of its Antigen-Binding Fragment in Free and Antigen-Complexed Forms Authors: Mylvaganam, S.E. / Paterson, Y. / Kaiser, K. / Bowdish, K. / Getzoff, E.D. #2: ![]() Title: Monoclonal Antibodies to Horse Cytochrome C Expressing Four Distinct Idiotypes Distribute Among Two Sites on the Native Protein Authors: Carbone, F.R. / Paterson, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131 KB | Display | ![]() |
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PDB format | ![]() | 102.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qblSC ![]() 1qbmC ![]() 1hrcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules F
#3: Protein | Mass: 11751.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OBTAINED FROM SIGMA / Source: (natural) ![]() ![]() |
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-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23655.057 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23851.572 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) ![]() ![]() |
-Non-polymers , 3 types, 639 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-HEM / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42 % | |||||||||||||||
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Crystal grow | pH: 6.4 Details: 50MM ZINC ACETATE BUFFER, PH 6.4, 25% (W/V) PEG 4000. | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 48348 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.06 Å2 / Rsym value: 0.084 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 12 / Rsym value: 0.282 / % possible all: 99.5 |
Reflection | *PLUS Num. obs: 48334 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 99.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2.26 A RESOLUTION FABE8 X-RAY STRUCTURE (FREE FAB E8) (MYLVAGANAM ET AL., 1998, JMB, 281, 301-32; PDB ENTRY 1QBL) AND HORSE CYTOCHROME C 1.9 A X-RAY STRUCTURE (BUSHNELL ET. AL., 1990; ...Starting model: 2.26 A RESOLUTION FABE8 X-RAY STRUCTURE (FREE FAB E8) (MYLVAGANAM ET AL., 1998, JMB, 281, 301-32; PDB ENTRY 1QBL) AND HORSE CYTOCHROME C 1.9 A X-RAY STRUCTURE (BUSHNELL ET. AL., 1990; PDB ENTRY 1HRC). Resolution: 1.8→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 21.96 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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