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Yorodumi- PDB-3cew: Crystal structure of a cupin protein (BF4112) from Bacteroides fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cew | ||||||
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Title | Crystal structure of a cupin protein (BF4112) from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR205 | ||||||
Components | Uncharacterized cupin protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / all beta-protein / jelly-roll (cupin-2) / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å | ||||||
Authors | Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Wang, H. / Baran, M.C. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Wang, H. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a cupin protein (BF4112) from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR205. Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Wang, H. / Baran, M.C. / 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 | 3cew.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cew.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cew_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 3cew_full_validation.pdf.gz | 467.9 KB | Display | |
Data in XML | 3cew_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 3cew_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/3cew ftp://data.pdbj.org/pub/pdb/validation_reports/ce/3cew | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13764.029 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF4112 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5L811, UniProt: A0A380YRY7*PLUS #2: Chemical | ChemComp-ZN / #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: 50.98 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM MES pH 6.0, 20% PEG 4000, 100 mM Magnesium chloride, MICROBATCH UNDER OIL, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2008 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / 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: 43936 / Num. obs: 43936 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.073 / Net I/σ(I): 30.36 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 13.38 / Num. unique all: 4634 / Rsym value: 0.124 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.31→19.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 529681.23 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.8914 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.38 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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