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Yorodumi- PDB-5d59: In meso X-ray crystallography structure of the PepTSt-Ala-Phe com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d59 | ||||||
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Title | In meso X-ray crystallography structure of the PepTSt-Ala-Phe complex at 100 K | ||||||
Components | Di-or tripeptide:H+ symporter | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / peptide transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Streptococcus thermophilus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Huang, C.-Y. / Olieric, V. / Wang, M. / Caffrey, M. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d59.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d59.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 5d59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d59_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 5d59_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 5d59_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 5d59_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d59 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d59 | HTTPS FTP |
-Related structure data
Related structure data | 5d52C 5d53C 5d54C 5d56C 5d57C 5d58C 5d5aC 5d5bC 5d5cC 5d5dC 5d5eC 5d5fC 4d2cS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52782.148 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) Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8 |
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-Non-polymers , 6 types, 101 molecules
#2: Chemical | ChemComp-ALA / | ||||||
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#3: Chemical | ChemComp-PHE / | ||||||
#4: Chemical | ChemComp-78M / ( #5: Chemical | ChemComp-PO4 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 250-325 mM NH4H2PO4, 100 mM HEPES, pH 7.0, 21-22 %(v/v) PEG 400 and 10 mM Ala-Phe PH range: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03321 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 24537 / % possible obs: 99.8 % / Redundancy: 4.41 % / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.36 % / Mean I/σ(I) obs: 2.26 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4d2c Resolution: 2.4→46.13 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.73 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→46.13 Å
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Refine LS restraints |
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LS refinement shell |
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