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Yorodumi- PDB-4hqs: Crystal structure of the pneumoccocal exposed lipoprotein thiored... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hqs | ||||||
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Title | Crystal structure of the pneumoccocal exposed lipoprotein thioredoxin sp_0659 (Etrx1) from Streptococcus pneumoniae strain TIGR4 | ||||||
Components | Thioredoxin family proteinThioredoxin domain | ||||||
Keywords | OXIDOREDUCTASE / lipoprotein / Disulfide Bridge / Thiorredoxin / membrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Bartual, S.G. / Saleh, M. / Abdullah, M.R. / Jensch, I. / Asmat, T.M. / Petruschka, L. / Pribyl, T. / Hermoso, J.A. / Hammerschmidt, S. | ||||||
Citation | Journal: EMBO Mol Med / Year: 2013 Title: Molecular architecture of Streptococcus pneumoniae surface thioredoxin-fold lipoproteins crucial for extracellular oxidative stress resistance and maintenance of virulence. Authors: Saleh, M. / Bartual, S.G. / Abdullah, M.R. / Jensch, I. / Asmat, T.M. / Petruschka, L. / Pribyl, T. / Gellert, M. / Lillig, C.H. / Antelmann, H. / Hermoso, J.A. / Hammerschmidt, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hqs.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hqs.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/4hqs ftp://data.pdbj.org/pub/pdb/validation_reports/hq/4hqs | HTTPS FTP |
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-Related 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: 21170.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0659 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97RX4, UniProt: A0A0H2UP26*PLUS | ||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→29.87 Å / Num. all: 30688 / Num. obs: 30641 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26.5 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 1.48→1.56 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→28.107 Å / SU ML: 0.16 / σ(F): 1.35 / 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 / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.48→28.107 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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