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Yorodumi- PDB-3fgb: Crystal structure of the Q89ZH8_BACTN protein from Bacteroides th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fgb | ||||||
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Title | Crystal structure of the Q89ZH8_BACTN protein from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR289b. | ||||||
Components | uncharacterized protein Q89ZH8_BACTN | ||||||
Keywords | structural genomics / unknown function / Q89ZH8_BACTN / BTR289B / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Vorobiev, S.M. / Lew, S. / Seetharaman, J. / Lee, D. / Foote, L.E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. ...Vorobiev, S.M. / Lew, S. / Seetharaman, J. / Lee, D. / Foote, L.E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Q89ZH8_BACTN protein from Bacteroides thetaiotaomicron. Authors: Vorobiev, S.M. / Lew, S. / Seetharaman, J. / Lee, D. / Foote, L.E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / 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 | 3fgb.cif.gz | 153 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fgb.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fgb_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 3fgb_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 3fgb_validation.xml.gz | 34 KB | Display | |
Data in CIF | 3fgb_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/3fgb ftp://data.pdbj.org/pub/pdb/validation_reports/fg/3fgb | 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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Details | monomer according to aggregation screening |
-Components
#1: Protein | Mass: 39589.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482 / Gene: BT_4399 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q89ZH8 #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: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 20000, 0.035M potassium chloride, 0.1M Tris.HCl, pH 8.0, 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: 0.97941, 0.97960, 0.96862 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2008 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. all: 94601 / Num. obs: 94128 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 4.5 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 18.6 | ||||||||||||
Reflection shell | Resolution: 2→2.14 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 7.3 / Num. unique all: 10495 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→42.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 198428.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.2651 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→42.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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