+Open data
-Basic information
Entry | Database: PDB / ID: 4pov | ||||||
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Title | ThiT with LMG135 bound | ||||||
Components | Thiamine transporter ThiT | ||||||
Keywords | PROTEIN BINDING / S-component / Thiamine-binding protein / ECF module / Membrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactococcus lactis subsp. cremoris (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Swier, L.J.Y.M. / Guskov, A. / Slotboom, D.J. | ||||||
Citation | Journal: Chembiochem / Year: 2015 Title: Structure-Based Design of Potent Small-Molecule Binders to the S-Component of the ECF Transporter for Thiamine. Authors: Swier, L.J. / Monjas, L. / Guskov, A. / de Voogd, A.R. / Erkens, G.B. / Slotboom, D.J. / Hirsch, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pov.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pov.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pov_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4pov_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4pov_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4pov_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/4pov ftp://data.pdbj.org/pub/pdb/validation_reports/po/4pov | HTTPS FTP |
-Related structure data
Related structure data | 4popC 3rlbS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 8 molecules AB
#1: Protein | Mass: 21231.480 Da / Num. of mol.: 2 / Fragment: ThiT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain: NZ9000 / Gene: llmg_0334, LLNZ_01755, thiT / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: A2RI47 #5: Sugar | ChemComp-BNG / |
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-Non-polymers , 9 types, 94 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / #6: Chemical | ChemComp-PEG / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-P6G / | #10: Chemical | ChemComp-CL / | #11: 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: 3.94 Å3/Da / Density % sol: 68.79 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.15 M NH4NO3, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.000002 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000002 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.042 Å / Num. all: 33341 / Num. obs: 33341 / % possible obs: 99.38 % / Observed criterion σ(I): 1 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.2→2.2648 Å / % possible all: 0.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3RLB Resolution: 2.2→48.042 Å / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→48.042 Å
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Refine LS restraints |
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