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Yorodumi- PDB-3lyy: Crystal structure of the MucBP domain of the adhesion protein PEP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lyy | ||||||
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Title | Crystal structure of the MucBP domain of the adhesion protein PEPE_0118 from Pediococcus pentosaceus. Northeast Structural Genomics Consortium target id PtR41A | ||||||
Components | Adhesion exoprotein | ||||||
Keywords | CELL ADHESION / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Cell wall / Peptidoglycan-anchor | ||||||
Function / homology | Function and homology information Immunoglobulin-like - #4300 / Mub B2-like domain / Muc B2-like domain / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Pediococcus pentosaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the MucBP domain of the adhesion protein PEPE_0118 from Pediococcus pentosaceus. Northeast Structural Genomics Consortium target id PtR41A Authors: Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.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 | 3lyy.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lyy.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lyy_validation.pdf.gz | 421.7 KB | Display | wwPDB validaton report |
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Full document | 3lyy_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 3lyy_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3lyy_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/3lyy ftp://data.pdbj.org/pub/pdb/validation_reports/ly/3lyy | 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: 11544.041 Da / Num. of mol.: 2 / Fragment: sequence database residues 796-902 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Strain: ATCC 25745 / 183-1w / Gene: PEPE_0118 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03HU7 #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: 2.93 Å3/Da / Density % sol: 57.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5M (NH4)2SO4, 20% PEG3000, pH 7, 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: Feb 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 52646 / Num. obs: 52646 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 4.8 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.053 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 15 / Num. unique all: 2701 / Rsym value: 0.34 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→32.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 93956.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.5872 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→32.32 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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