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Yorodumi- PDB-2p0v: Crystal structure of BT3781 protein from Bacteroides thetaiotaomi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p0v | ||||||
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Title | Crystal structure of BT3781 protein from Bacteroides thetaiotaomicron, Northeast Structural Genomics Target BtR58 | ||||||
Components | Hypothetical protein BT3781Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Liu, J. / 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 BT3781 protein from Bacteroides thetaiotaomicron. Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Liu, J. / 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 | 2p0v.cif.gz | 193.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p0v.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/2p0v ftp://data.pdbj.org/pub/pdb/validation_reports/p0/2p0v | 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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Unit cell |
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-Components
#1: Protein | Mass: 56644.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Species: Bacteroides thetaiotaomicron / Strain: VPI-5482, DSM 2079, NCTC 10582, E50 / Gene: BT3781 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8A185 #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: 2.04 Å3/Da / Density % sol: 39.6 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris-HCl, 20% PEG 4000, 100 mM Potassium bromide, 5 mM DTT, pH 8, 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: 0.97912 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.61 Å / Num. all: 99728 / Num. obs: 99728 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.055 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.08 / Num. unique all: 10186 / Rsym value: 0.173 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→29.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 476106.02 / 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 FOR PHASING. XtalView program has also been used in refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.3926 Å2 / ksol: 0.348131 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
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