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Yorodumi- PDB-2ffg: Novel x-ray structure of the YkuJ protein from Bacillus subtilis.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ffg | ||||||
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Title | Novel x-ray structure of the YkuJ protein from Bacillus subtilis. Northeast Structural Genomics target SR360. | ||||||
Components | ykuJ | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / X-Ray SR360 NESG YkuJ / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Protein of unknown function DUF1797 / YkuJ-like / YkuJ-like superfamily / Protein of unknown function (DUF1797) / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YkuJ Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å | ||||||
Authors | Kuzin, A.P. / Abashidze, M. / Forouhar, F. / Vorobiev, S.M. / Ho, C.K. / Janjua, H. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. ...Kuzin, A.P. / Abashidze, M. / Forouhar, F. / Vorobiev, S.M. / Ho, C.K. / Janjua, H. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Novel x-ray structure of the YkuJ protein from Bacillus subtilis. Northeast Structural Genomics target SR360. Authors: Kuzin, A.P. / Abashidze, M. / Forouhar, F. / Vorobiev, S.M. / Ho, C.K. / Janjua, H. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J. ...Authors: Kuzin, A.P. / Abashidze, M. / Forouhar, F. / Vorobiev, S.M. / Ho, C.K. / Janjua, H. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ffg.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ffg.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ffg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ffg_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 2ffg_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 2ffg_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2ffg_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ffg ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ffg | 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: 10510.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ykuJ / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: O34588 #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: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM Ca-acetate, 18% PEG3350, 100 mM Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2005 / Details: Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 16561 / Num. obs: 16008 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 5.7 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.31→19.82 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 356919.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.3946 Å2 / ksol: 0.292296 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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