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Yorodumi- PDB-2i2l: X-ray Crystal Structure of Protein yopX from Bacillus subtilis. N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i2l | ||||||
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Title | X-ray Crystal Structure of Protein yopX from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR411. | ||||||
Components | YopX protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / SR411 / yopX / O34401 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information Complement Module; domain 1 - #50 / YopX protein / YopX protein / Complement Module; domain 1 / SH3 type barrels. - #100 / SH3 type barrels. / Ribbon / Roll / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Forouhar, F. / Kuzin, A.A. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. ...Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Forouhar, F. / Kuzin, A.A. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Acton, T. / 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 yopX from Bacillus subtilis Authors: Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Forouhar, F. / Kuzin, A.A. / Ho, C.K. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Acton, T. / 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 | 2i2l.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i2l.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 2i2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/2i2l ftp://data.pdbj.org/pub/pdb/validation_reports/i2/2i2l | HTTPS FTP |
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-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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16420.863 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yopX / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O34401 #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: 2.54 Å3/Da / Density % sol: 51.51 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 4000, 0.2M Sodium acetate, 0.2M Sodium thiocyanate, 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: 0.97911, 0.97944, 0.96798 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. all: 23997 / Num. obs: 23973 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.101 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→28.73 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 214814.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.3194 Å2 / ksol: 0.255885 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→28.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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