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- PDB-7mtt: Crystal structure of colibactin self-resistance protein ClbS in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mtt | ||||||
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Title | Crystal structure of colibactin self-resistance protein ClbS in complex with two molecules of CHES | ||||||
![]() | Colibactin self-protection protein ClbS | ||||||
![]() | DNA BINDING PROTEIN / hydrolase / DNA repair | ||||||
Function / homology | Protein of unknown function DUF1706 / Protein of unknown function (DUF1706) / DinB/YfiT-like putative metalloenzymes / Colibactin self-protection protein ClbS![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tripathi, P. / Bruner, S.D. | ||||||
![]() | ![]() Title: Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA. Authors: Tripathi, P. / Bruner, S.D. #1: ![]() Title: ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance Authors: Tripathi, P. / Bruner, S.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.8 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 940.2 KB | Display | ![]() |
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Full document | ![]() | 941.3 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mtlC ![]() 6anrS 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: 20747.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: clbS, APU18_08100, AWF59_018730, AZZ83_004503, CT146_21495, CUB99_02165, D3C88_24730, DNR41_00045, DNX30_29170, DS966_21615, DU333_02935, DW236_02620, ELT23_23590, ELT33_24270, EPS70_02685, ...Gene: clbS, APU18_08100, AWF59_018730, AZZ83_004503, CT146_21495, CUB99_02165, D3C88_24730, DNR41_00045, DNX30_29170, DS966_21615, DU333_02935, DW236_02620, ELT23_23590, ELT33_24270, EPS70_02685, EPS94_00180, EWK56_23755, FPI65_12320, FQU83_11985, GFU47_04510, GP945_05010, GP946_20500, HHG54_004716, HHJ44_00090, HJL93_000008, HJM41_001166, HJO44_004707, HJS53_002303, HmCmsJML146_00176, HNX34_25610, HV055_09710, HV098_09980, HV348_09415, NCTC9075_02752, NCTC9434_01964 Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES, pH 9.5, and 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→44.62 Å / Num. obs: 17844 / % possible obs: 99.58 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.85→1.915 Å / Num. unique obs: 1713 / CC1/2: 0.961 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ANR Resolution: 1.85→44.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.265 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 93.59 Å2 / Biso mean: 36.132 Å2 / Biso min: 19.37 Å2
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Refinement step | Cycle: final / Resolution: 1.85→44.62 Å
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LS refinement shell | Resolution: 1.85→1.897 Å / Rfactor Rfree error: 0
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