+Open data
-Basic information
Entry | Database: PDB / ID: 4mhw | ||||||
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Title | Crystal structure of ThiT with small molecule BAT-25 | ||||||
Components | Thiamine transporter ThiT | ||||||
Keywords | THIAMINE BINDING PROTEIN / S-component / ECF transporter / ABC transporter / substrate binding domain for thiamin / TRANSPORT PROTEIN | ||||||
Function / homology | Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha / Chem-0YN / DI(HYDROXYETHYL)ETHER / : Function and homology information | ||||||
Biological species | Lactococcus lactis subsp. cremoris (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Swier, L.J.Y.M. / Guskov, A. / Slotboom, D.J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of ThiT with small molecules modulators Authors: Swier, L.J.Y.M. / Gomez, L. / Guskov, A. / Hirsch, A.K.H. / Slotboom, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mhw.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mhw.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mhw_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4mhw_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4mhw_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4mhw_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/4mhw ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mhw | HTTPS FTP |
-Related structure data
Related structure data | 3rlbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 21231.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain: NZ9000 / Gene: LLNZ_01755 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: D8KFM5 #3: Sugar | |
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-Non-polymers , 8 types, 84 molecules
#2: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-PE4 / | #8: Chemical | ChemComp-PG0 / #9: Chemical | ChemComp-PG4 / #10: 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: 4.05 Å3/Da / Density % sol: 69.64 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.15 M ammonium nitrate, 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: 0.97625 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013 |
Radiation | Monochromator: liquid nitrogen cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.8 Å / Num. all: 23570 / Num. obs: 23465 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 1.57 / Num. unique all: 23570 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RLB Resolution: 2.5→42.799 Å / SU ML: 0.3 / σ(F): 1.99 / Phase error: 26.15 / 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: 2.5→42.799 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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