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Yorodumi- PDB-2ibo: X-ray Crystal Structure of Protein SP2199 from Streptococcus pneu... -
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-Basic information
Entry | Database: PDB / ID: 2ibo | ||||||
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Title | X-ray Crystal Structure of Protein SP2199 from Streptococcus pneumoniae. Northeast Structural Genomics Consortium Target SpR31 | ||||||
Components | Hypothetical protein SP2199 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Thiamine-binding protein / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Thiamine_BP domain-containing protein / Thiamine_BP domain-containing protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae TIGR4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Seetharaman, J. / Abashidze, M. / Forouhar, F. / Shastry, R. / Conover, K. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Abashidze, M. / Forouhar, F. / Shastry, R. / Conover, K. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the hypothetical protein SP2199 from Streptococcus pneumoniae, Northeast structural genomics target SpR31 Authors: Seetharaman, J. / Abashidze, M. / Forouhar, F. / Shastry, R. / Conover, K. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ibo.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ibo.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ibo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ibo_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 2ibo_full_validation.pdf.gz | 478.6 KB | Display | |
Data in XML | 2ibo_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 2ibo_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/2ibo ftp://data.pdbj.org/pub/pdb/validation_reports/ib/2ibo | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11938.139 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Species: Streptococcus pneumoniae / Strain: TIGR4, ATCC BAA-334 / Gene: SP_2199 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q97N67, UniProt: A0A0H2USK2*PLUS #2: 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: 3.46 Å3/Da / Density % sol: 64.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 18% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915, 0.97942, 0.96783 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2006 / Details: Mirrors | ||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. all: 31269 / Num. obs: 30208 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.082 / Net I/σ(I): 10.7 | ||||||||||||
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 11.7 / Num. unique all: 3482 / Rsym value: 0.406 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→45.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 65805.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.4838 Å2 / ksol: 0.355786 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→45.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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