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Yorodumi- PDB-7egt: The crystal structure of the C-terminal domain of T. thermophilus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7egt | ||||||
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Title | The crystal structure of the C-terminal domain of T. thermophilus UvrD complexed with the N-terminal domain of UvrB | ||||||
Components |
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Keywords | TRANSCRIPTION / TCR / Thermus thermophilus / RNA polymerase / UvrD / UvrB / DNA repair | ||||||
Function / homology | Function and homology information excinuclease ABC activity / excinuclease repair complex / SOS response / DNA helicase activity / nucleotide-excision repair / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.581 Å | ||||||
Authors | Zheng, F. / Shen, L. / Li, L. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2022 Title: Crucial role and mechanism of transcription-coupled DNA repair in bacteria. Authors: Bharati, B.K. / Gowder, M. / Zheng, F. / Alzoubi, K. / Svetlov, V. / Kamarthapu, V. / Weaver, J.W. / Epshtein, V. / Vasilyev, N. / Shen, L. / Zhang, Y. / Nudler, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7egt.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7egt.ent.gz | 150.3 KB | Display | PDB format |
PDBx/mmJSON format | 7egt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7egt_validation.pdf.gz | 459.2 KB | Display | wwPDB validaton report |
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Full document | 7egt_full_validation.pdf.gz | 468 KB | Display | |
Data in XML | 7egt_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 7egt_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/7egt ftp://data.pdbj.org/pub/pdb/validation_reports/eg/7egt | HTTPS FTP |
-Related structure data
Related structure data | 7egsC 1d2mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: Protein | Mass: 47175.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: uvrB, TTHA1892 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56243 #2: Protein | Mass: 6420.366 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: uvrD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O24736, DNA helicase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 22, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.58→50 Å / Num. obs: 41725 / % possible obs: 98.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Χ2: 1.193 / Net I/σ(I): 5.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D2M Resolution: 2.581→46.166 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.88 Å2 / Biso mean: 62.5845 Å2 / Biso min: 36.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.581→46.166 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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