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Open data
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Basic information
Entry | Database: PDB / ID: 1bgx | ||||||
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Title | TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB | ||||||
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![]() | COMPLEX (POLYMERASE/INHIBITOR) / DNA POLYMERASE / FAB / PCR / INHIBITION / HELIX-COIL DYNAMICS / INHIBITOR DESIGN / COMPLEX (POLYMERASE-INHIBITOR) / COMPLEX (POLYMERASE-INHIBITOR) complex | ||||||
Function / homology | ![]() nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Murali, R. / Sharkey, D.J. / Daiss, J.L. / Krishna Murthy, H.M. | ||||||
![]() | ![]() Title: Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme. Authors: Murali, R. / Sharkey, D.J. / Daiss, J.L. / Murthy, H.M. #1: ![]() Title: Structural Studies on an Inhibitory Antibody Against Thermus Aquaticus DNA Polymerase Suggest Mode of Inhibition Authors: Murali, R. / Helmer-Citterich, M. / Sharkey, D.J. / Scalice, E.R. / Daiss, J.L. / Sullivan, M.A. / Krishna Murthy, H.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 | ![]() | 258.5 KB | Display | ![]() |
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PDB format | ![]() | 207.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.1 KB | Display | ![]() |
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Full document | ![]() | 410 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 40.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 94046.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23082.521 Da / Num. of mol.: 1 / Fragment: FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Antibody | Mass: 23590.266 Da / Num. of mol.: 1 / Fragment: FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PROTEIN WAS CRYSTALLIZED FROM 22% PEG 3350, 200 MM TRIS/HCL, PH 7.4. COMPLEX WAS MADE AT A PROTEIN CONCENTRATION OF 0.5 MG/ML, LEFT FOR 2-3 DAYS AT 4 DEGREES CELSIUS, CONCENTRATED TO 5MG/ML ...Details: PROTEIN WAS CRYSTALLIZED FROM 22% PEG 3350, 200 MM TRIS/HCL, PH 7.4. COMPLEX WAS MADE AT A PROTEIN CONCENTRATION OF 0.5 MG/ML, LEFT FOR 2-3 DAYS AT 4 DEGREES CELSIUS, CONCENTRATED TO 5MG/ML PROTEIN AND CRYSTALLIZATION CARRIED OUT IN HANGING DROPS., vapor diffusion - hanging drop, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→27.7 Å / Num. obs: 81111 / % possible obs: 82 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 8 / % possible all: 75.9 |
Reflection | *PLUS Num. measured all: 414722 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AYL AND 1TAQ Resolution: 2.3→8 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 100000 / Data cutoff low absF: 1.0E-5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 28.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.25 |