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Open data
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Basic information
Entry | Database: PDB / ID: 1yuh | ||||||
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Title | FAB FRAGMENT | ||||||
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![]() | IMMUNE SYSTEM / ANTI-NITROPHENOL / LAMBDA LIGHT CHAIN / IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-NP / : / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Yuhasz, S.C. / Amzel, L.M. / Parry, C. / Strand, M. | ||||||
![]() | ![]() Title: Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody. Authors: Yuhasz, S.C. / Parry, C. / Strand, M. / Amzel, L.M. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of an Anti-4-Hydroxy-3-Nitrophenylacetic Acid Monoclonal Antibody Fab Fragment Complexed with Immunizing and Heteroclitic Haptens Authors: Yuhasz, S.C. / Ysern, X. / Strand, M. / Amzel, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.1 KB | Display | ![]() |
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PDB format | ![]() | 137.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507 KB | Display | ![]() |
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Full document | ![]() | 578.6 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 22672.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23434.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - ...IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.52 / Method: vapor diffusion, hanging drop / Details: Yuhasz, S.C., (1989) J.Mol.Biol., 209, 319. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 16470 / % possible obs: 70.3 % / Rmerge(I) obs: 0.047 |
Reflection | *PLUS Highest resolution: 3 Å |
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Processing
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Refinement | Resolution: 3→6 Å / σ(F): 2 Details: IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. ...Details: IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. MOLECULE 2 DEFINES THE LIGHT CHAIN RESIDUES AS VL2 2 - 109, CL2 110 - 212, AND HEAVY CHAIN RESIDUES AS VH2 1 - 117 AND CH2 118 - 218, RESPECTIVELY. THE WATERS ARE NUMBERED 990 - 994 AND THE 2 NITROPHENOL-EPSILON-AMINO CAPROIC MOLECULES LABELED AS NP ARE NUMBERED 995 AND 996. RESIDUES NUMBERED 132 - 140 OF H AND B CHAINS WERE NOT FOUND IN THE ELECTRON DENSITY AND ARE PROBABLY DISORDERED.
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |