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Yorodumi- PDB-7ac6: Structure of sponge-phase grown PepTst2 collected by rotation ser... -
+Open data
-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 | ||||||
Components | (Di-or tripeptide:H+ ...) x 2 | ||||||
Keywords | TRANSPORT PROTEIN / peptide transport protein | ||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Streptococcus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Martiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Wang, M. / Marsh, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ac6.cif.gz | 135.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ac6.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ac6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/7ac6 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/7ac6 | HTTPS FTP |
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-Related structure data
Related structure data | 7ac2C 7ac3C 7ac4C 7ac5C 7ai8C 7ai9C 4xnjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria) Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8 |
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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.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria) Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) |
-Non-polymers , 5 types, 41 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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