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- PDB-1dzb: Crystal structure of phage library-derived single-chain Fv fragme... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dzb | ||||||
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Title | Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme | ||||||
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![]() | IMMUNE SYSTEM / COMPLEX (ANTIBODY ANTIGEN) / SINGLE-DOMAIN ANTIBODY / TURKEY EGG-WHITE LYSOZYME / ANTIBODY- PROTEIN COMPLEX / SINGLE-CHAIN FV FRAGMENT | ||||||
Function / homology | ![]() glycosaminoglycan binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ay, J. / Keitel, T. / Kuettner, G. / Wessner, H. / Scholz, C. / Hahn, M. / Hoehne, W. | ||||||
![]() | ![]() Title: Crystal Structure of a Phage Library-Derived Single-Chain Fv Fragment Complexed with Turkey Egg -White Lysozyme at 2.0 A Resolution Authors: Ay, J. / Keitel, T. / Kuttner, G. / Wessner, H. / Scholz, C. / Hahn, M. / Hohne, W. #1: Journal: Mol.Immunol. / Year: 1998 Title: A Phage Library-Derived Single-Chain Fv Fragment in Complex with a Phage Library-Derived Single-Chain Fv Fragment in Complex Withturkey Egg-White Lysozyme: Characterization, Crystallization ...Title: A Phage Library-Derived Single-Chain Fv Fragment in Complex with a Phage Library-Derived Single-Chain Fv Fragment in Complex Withturkey Egg-White Lysozyme: Characterization, Crystallization Andpreliminary X-Ray Analysis Authors: Kuttner, G. / Keitel, T. / Giessmann, E. / Wessner, H. / Scholz, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.8 KB | Display | ![]() |
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PDB format | ![]() | 119.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jhlS S: Starting model for refinement |
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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: 27253.922 Da / Num. of mol.: 2 / Fragment: SEE REMARK 400 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 14228.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Water | ChemComp-HOH / | Compound details | CHAIN A,B: EACH CHAIN IS MADE UP FROM: RESIDUES 1-116: HEAVY CHAIN VARIABLE REGION OF 1F9 RESIDUES ...CHAIN A,B: EACH CHAIN IS MADE UP FROM: RESIDUES 1-116: HEAVY CHAIN VARIABLE REGION OF 1F9 RESIDUES 117-131: GGGGSGGGGS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 35.6 % Description: THERE ARE TWO MOLECULE COMPLEXES PER ASYMMETRIC UNIT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND ...Details: A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND EQUILIBRATED AGAINST 30% PEG4000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 55.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / pH: 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.045 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 40240 / % possible obs: 87.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.683 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.77 / % possible all: 75.5 |
Reflection | *PLUS Num. measured all: 297921 |
Reflection shell | *PLUS % possible obs: 75.5 % / Num. unique obs: 3449 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JHL Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THERE ARE TWO MOLECULES PER ASYMMETRIC UNIT
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Displacement parameters | Biso mean: 32.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |