+Open data
-Basic information
Entry | Database: PDB / ID: 4d2d | ||||||
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Title | Structure of a tri peptide bound POT family peptide transporter | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / MAJOR FACILITATOR SUPERFAMILY / PROTON OLIGOPEPTIDE TRANSPORTER (POT) FAMILY / PEPTIDE TRANSPORTER / TRIPEPTIDE COMPLEX | ||||||
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: 2.522 Å | ||||||
Authors | Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T.A. / Caffrey, M. / Newstead, S. | ||||||
Citation | Journal: Embo Rep. / Year: 2014 Title: Structural Basis for Polyspecificity in the Pot Family of Proton-Coupled Oligopeptide Transporters. Authors: Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T. / Caffrey, M. / Newstead, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d2d.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d2d.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 4d2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d2d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4d2d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4d2d_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4d2d_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/4d2d ftp://data.pdbj.org/pub/pdb/validation_reports/d2/4d2d | HTTPS FTP |
-Related structure data
Related structure data | 4d2bC 4d2cC 4apsS C: citing same article (ref.) S: Starting model for refinement |
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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 / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 53721.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS THERMOPHILUS (bacteria) / Strain: LMG 18311 / Plasmid: PWALDO-GFPD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q5M4H8 |
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#2: Protein/peptide | Mass: 231.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 52 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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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: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE |
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Crystal grow | Method: lipidic cubic phase / pH: 7 Details: 16-23 %(V/V) PEG 400, 0.1 M HEPES PH 7.0, 0.15-0.55 M NH4H2PO4 AND 10 MM TRI-ALANINE. CRYSTALS WERE GROWN BY THE LCP METHOD WITH 7.8 MAG AS HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 2, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→75.56 Å / Num. obs: 21341 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 44.26 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.52→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4APS Resolution: 2.522→75.556 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 24.67 / Stereochemistry target values: ML Details: RESIDUES 1-5, 272-275, 414-419, 479-491 ARE DISORDERED TRIPEPTIDE WAS MODELED WITH ITS C-TERMINUS ORIENTATED TOWARDS THE EXTRACELLULAR SIDE. SEE PAPER FOR FURTHER DISCUSSION.
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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: 50.229 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.522→75.556 Å
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Refine LS restraints |
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LS refinement shell |
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