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- PDB-6a9k: Crystal structure of the complex of the hydrolytic antibody Fab 9... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a9k | ||||||
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Title | Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog | ||||||
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![]() | IMMUNE SYSTEM / Catalytic Antibody / Hydrolytic Antibody / 9C10 / Fab / Complex / Transition-State Analog | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-9T0![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsuchiya, Y. / Fujii, I. / Tada, T. / Yamaguchi, A. / Tsumuraya, T. / Kumon, A. | ||||||
![]() | ![]() Title: Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog Authors: Tsuchiya, Y. / Fujii, I. / Tada, T. / Yamaguchi, A. / Tsumuraya, T. / Kumon, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.6 KB | Display | ![]() |
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PDB format | ![]() | 148.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dtmS 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: 24131.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Antibody | Mass: 23922.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 50 mM Tris-HCl, 25% PEG 3350, 0.1 mM EDTA, pH8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 59706 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.063 / Rrim(I) all: 0.167 / Χ2: 1.039 / Net I/av σ(I): 15.9 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3012 / CC1/2: 0.774 / Rpim(I) all: 0.397 / Rrim(I) all: 1.005 / Χ2: 1.004 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DTM Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.669 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.172 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.642 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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