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Yorodumi- PDB-3l6i: Crystal structure of the uncharacterized lipoprotein yceb from e.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l6i | |||||||||
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Title | Crystal structure of the uncharacterized lipoprotein yceb from e. coli at the resolution 2.0a. northeast structural genomics consortium target er542 | |||||||||
Components | Uncharacterized lipoprotein yceB | |||||||||
Keywords | structure genomics / unknown function / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Cell membrane / Lipoprotein / Membrane / Palmitate | |||||||||
Function / homology | Uncharacterised protein PF07273 family, DUF1439 / Protein of unknown function DUF1439 / Protein of unknown function (DUF1439) / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Alpha Beta / Uncharacterized lipoprotein YceB Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.011 Å | |||||||||
Authors | Kuzin, A.P. / Neely, H. / Seetharaman, J. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Neely, H. / Seetharaman, J. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of the uncharacterized lipoprotein yceb from e. coli at the resolution 2.0a. northeast structural genomics consortium target er542 Authors: Kuzin, A.P. / Neely, H. / Seetharaman, J. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l6i.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l6i.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 3l6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l6i_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 3l6i_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 3l6i_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3l6i_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/3l6i ftp://data.pdbj.org/pub/pdb/validation_reports/l6/3l6i | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20740.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yceB, b1063, JW1050 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: P0AB26 #2: Chemical | #3: 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: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.3M NA MALONATE, 0.05M BIS TRIS, PROPANE PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: Aug 14, 2008 / Details: mirror |
Radiation | Monochromator: MONOCHROMATIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→19.89 Å / Num. obs: 50815 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.011→19.793 Å / SU ML: 0.3 / σ(F): 1 / Phase error: 23.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.168 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.011→19.793 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 27.7927 Å / Origin y: 85.8457 Å / Origin z: 23.7622 Å
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Refinement TLS group | Selection details: all |