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- PDB-2duy: Crystal structure of competence protein ComEA-related protein fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2duy | ||||||
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Title | Crystal structure of competence protein ComEA-related protein from Thermus thermophilus HB8 | ||||||
![]() | Competence protein ComEA-related protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HELIX-HAIRPIN-HELIX / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Photosystem II 12 kDa extrinsic protein / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / DNA polymerase; domain 1 / DNA repair / DNA binding / Orthogonal Bundle / Mainly Alpha / Competence protein ComEA-related protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niwa, H. / Shimada, A. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Ebihara, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of competence protein ComEA-related protein from Thermus thermophilus HB8 Authors: Niwa, H. / Shimada, A. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Ebihara, A. / Yokoyama, 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 | ![]() | 21.6 KB | Display | ![]() |
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PDB format | ![]() | 15.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.8 KB | Display | ![]() |
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Full document | ![]() | 420.8 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 8287.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. all: 5420 / Num. obs: 5420 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 69.2 | ||||||||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 10.2 / Num. unique all: 522 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.246 Å2 / ksol: 0.354968 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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