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- PDB-7ac6: Structure of sponge-phase grown PepTst2 collected by rotation ser... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ac6 | ||||||
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Title | Structure of sponge-phase grown PepTst2 collected by rotation serial crystallography on a COC membrane at a synchrotron source | ||||||
![]() | (Di-or tripeptide:H+ ...) x 2 | ||||||
![]() | TRANSPORT PROTEIN / peptide transport protein | ||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Wang, M. / Marsh, M. | ||||||
![]() | ![]() Title: Versatile microporous polymer-based supports for serial macromolecular crystallography. Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.6 KB | Display | ![]() |
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PDB format | ![]() | 87.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 547 KB | Display | ![]() |
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Full document | ![]() | 514.3 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ac2C ![]() 7ac3C ![]() 7ac4C ![]() 7ac5C ![]() 7ai8C ![]() 7ai9C ![]() 4xnjS 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
-Di-or tripeptide:H+ ... , 2 types, 2 molecules AY
#1: Protein | Mass: 52237.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 236.267 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: ![]() ![]() |
-Non-polymers , 5 types, 41 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PO4 / | ||||||
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#4: Chemical | ChemComp-78M / ( #5: Chemical | ChemComp-PG0 / | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 325 mM NH4H2PO4, 100 mM HEPES pH 7.0, 21-22%(v/v) PEG 400 and 10 mM dipeptide, AF |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.26 Å / Num. obs: 12579 / % possible obs: 94.7 % / Redundancy: 3.05 % / Biso Wilson estimate: 70.78 Å2 / CC1/2: 0.974 / Net I/σ(I): 3.84 |
Reflection shell | Resolution: 3→3.08 Å / Mean I/σ(I) obs: 0.78 / Num. unique obs: 1192 / CC1/2: 0.217 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XNJ Resolution: 3→49.26 Å / SU ML: 0.5161 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.132 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 67.33 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.26 Å
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Refine LS restraints |
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LS refinement shell |
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