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Open data
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Basic information
Entry | Database: PDB / ID: 5g4q | ||||||
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Title | H.pylori Beta clamp in complex with 5-chloroisatin | ||||||
![]() | DNA POLYMERASE III SUBUNIT BETA | ||||||
![]() | TRANSFERASE / DNA SLIDING CLAMP / PROCESSIVITY PROMOTING FACTOR | ||||||
Function / homology | ![]() DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pandey, P. / Gourinath, S. | ||||||
![]() | ![]() Title: Screening of E. coli beta-clamp Inhibitors Revealed that Few Inhibit Helicobacter pylori More Effectively: Structural and Functional Characterization. Authors: Pandey, P. / Verma, V. / Dhar, S.K. / Gourinath, S. #1: ![]() Title: Structural Insight Into Beta-Clamp and its Interaction with DNA Ligase in Helicobacter Pylori. Authors: Pandey, P. / Tarique, K.F. / Mazumder, M. / Rehman, S.A.A. / Kumari, N. / Gourinath, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.7 KB | Display | ![]() |
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PDB format | ![]() | 118.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 460.1 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fveC ![]() 5fxtC ![]() 4rkiS 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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Unit cell |
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Components
#1: Protein | Mass: 42238.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: BETA CLAMP IN COMPLEX WITH 5-CHLOROISATIN / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-2HQ / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % Description: THIS DATA WAS OBTAINED FROM CRYSTALS SOAKED IN LIGAND BEFORE DIFFRACTION LEADING TO HIGH TEMPERATURE FACTOR AND LOW OCCUPANCY |
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Crystal grow | Details: 6% W/V PEG 20,000, 20% V/V PEG 550MME, 0.01M MGCL2, 0.1M MOPS/ HEPES-NA PH7.3, 0.2M AMMONIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 39777 / % possible obs: 91.1 % / Observed criterion σ(I): 0.3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.3→50 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 92.8 |
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Processing
Software | Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB NETRY 4RKI Resolution: 2.3→80 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA OBTAINED FROM CRYSTALS SOAKED WITH LIGAND LEADING TO HIGH TEMPERATURE FACTOR AND LOW OCCUPANCY.
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Refinement step | Cycle: LAST / Resolution: 2.3→80 Å
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