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Yorodumi- PDB-2dlb: X-ray Crystal Structure of Protein yopT from Bacillus subtilis. N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dlb | ||||||
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Title | X-ray Crystal Structure of Protein yopT from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR412 | ||||||
Components | yopT | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / sr412 / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Protein of unknown function YopT / Protein of unknown function YopT / YopT domain superfamily / Hypothetical protein Yopt / Ubiquitin-like (UB roll) / Roll / Alpha Beta / SPbeta prophage-derived uncharacterized protein YopT Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.2 Å | ||||||
Authors | Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be published Title: X-ray structure of hypothetical protein from Bacillus subtilis O34498 at the resolution of 1.2A. NESG target SR412 Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.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 | 2dlb.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dlb.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dlb_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 2dlb_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 2dlb_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2dlb_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/2dlb ftp://data.pdbj.org/pub/pdb/validation_reports/dl/2dlb | 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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Details | In according to Dynamic Light Scattering SR412 is dimer. |
-Components
#1: Protein | Mass: 9249.060 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pE21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O34498 #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: 2.71 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1M lithium sulfate, 0.1M sodium citrate, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9787, 0.9794, 0.9678 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2006 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.2→30 Å / Num. all: 53757 / Num. obs: 53730 / % possible obs: 87.5 % / Observed criterion σ(I): -3 | ||||||||||||
Reflection shell | Resolution: 1.2→1.24 Å / % possible all: 59.6 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.2→30 Å / Num. parameters: 11721 / Num. restraintsaints: 14189 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: Anisotropic refinement reduced free r (no cutoff) by
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1100.5 / Occupancy sum non hydrogen: 1281 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→30 Å
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Refine LS restraints |
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