+Open data
-Basic information
Entry | Database: PDB / ID: 5d6k | |||||||||
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Title | PepT - CIM | |||||||||
Components | Di-or tripeptide:H+ symporter | |||||||||
Keywords | TRANSPORT PROTEIN / ALPHA-HELICAL / Major Facilitator Superfamily (MFS) Transporters / PepTSt Oligopeptide-proton symporter (POT family) | |||||||||
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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Ma, P. / Caffrey, M. | |||||||||
Funding support | Ireland, Belgium, 2items
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Citation | Journal: Nat Protoc / Year: 2017 Title: The cubicon method for concentrating membrane proteins in the cubic mesophase. Authors: Ma, P. / Weichert, D. / Aleksandrov, L.A. / Jensen, T.J. / Riordan, J.R. / Liu, X. / Kobilka, B.K. / Caffrey, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6k.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6k.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 5d6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d6k_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5d6k_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5d6k_validation.xml.gz | 19 KB | Display | |
Data in CIF | 5d6k_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6k ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6k | HTTPS FTP |
-Related structure data
Related structure data | 5d6iC 5d6lC 5iyuC 4d2bS 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
#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) Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5M4H8 | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | ChemComp-97M / ( #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 17-22.5 %(V/V) PEG 400, 0.1 M HEPES PH 7.0 AND 0.15-0.48 M NH4H2PO4. CRYSTALS WERE GROWN BY THE LCP METHOD USING 9.7 MAG AS HOSTING LIPID. PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50.85 Å / Num. obs: 25142 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D2B Resolution: 2.4→50.845 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2 / 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→50.845 Å
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Refine LS restraints |
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LS refinement shell |
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