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Yorodumi- PDB-3bjv: The Crystal Structure of a putative PTS IIA(PtxA) from Streptococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bjv | ||||||
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Title | The Crystal Structure of a putative PTS IIA(PtxA) from Streptococcus mutans | ||||||
Components | RmpA | ||||||
Keywords | TRANSFERASE / alpha/beta three layer sandwich | ||||||
Function / homology | PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta / PTS ascorbate transporter subunit IIA Function and homology information | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Lei, J. / Liang, Y.H. / Su, X.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structures of phosphotransferase system enzymes PtxB (IIB(Asc)) and PtxA (IIA(Asc)) from Streptococcus mutans Authors: Lei, J. / Li, L.-F. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bjv.cif.gz | 43.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bjv.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bjv_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 3bjv_full_validation.pdf.gz | 423.9 KB | Display | |
Data in XML | 3bjv_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3bjv_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjv ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjv | HTTPS FTP |
-Related structure data
Related structure data | 3czcC 2oqtS 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: 17696.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: ptxA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q93DA9, protein-Npi-phosphohistidine-sugar phosphotransferase |
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#2: 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: 2.05 Å3/Da / Density % sol: 40.07 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.9 Details: 0.1M Tris-Hcl, 1.9-2.1M (NH4)2SO4, pH 7.9, Vapor diffusion, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Dec 2, 2007 |
Radiation | Monochromator: multilayer mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40.65 Å / Num. all: 6206 / Num. obs: 6026 / % possible obs: 97.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.0717 / Rsym value: 0.0717 / Net I/σ(I): 10.08 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 9 % / Rmerge(I) obs: 0.1297 / Mean I/σ(I) obs: 0.1297 / Num. unique all: 897 / Rsym value: 0.1297 / % possible all: 85.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OQT Resolution: 2.4→27.28 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.265 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.114 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.719 Å2
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Refine analyze | Luzzati coordinate error obs: 0.232 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→27.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.397→2.459 Å / Total num. of bins used: 20
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