+Open data
-Basic information
Entry | Database: PDB / ID: 3tu8 | ||||||
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Title | Crystal Structure of the Burkholderia Lethal Factor 1 (BLF1) | ||||||
Components | Burkholderia Lethal Factor 1 (BLF1) | ||||||
Keywords | UNKNOWN FUNCTION / toxin | ||||||
Function / homology | Burkholderia lethal factor 1 / Burkholderia lethal factor 1 / BROMIDE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.04 Å | ||||||
Authors | Cruz, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Chang, C.T. / Mahadi, N.M. / Mobbs, G.W. / Mohamed, R. / Nathan, S. / Partridge, L.J. ...Cruz, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Chang, C.T. / Mahadi, N.M. / Mobbs, G.W. / Mohamed, R. / Nathan, S. / Partridge, L.J. / Raih, M.F. / Ruzheinikov, S.N. / Sedelnikova, S.E. / Wilson, S.A. / Rice, D.W. | ||||||
Citation | Journal: Science / Year: 2011 Title: A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A. Authors: Cruz-Migoni, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Bokori-Brown, M. / Chang, C.T. / Dickman, M.J. / Essex-Lopresti, A. / Harding, S.V. / Mahadi, N.M. / Marshall, L.E. / ...Authors: Cruz-Migoni, A. / Hautbergue, G.M. / Artymiuk, P.J. / Baker, P.J. / Bokori-Brown, M. / Chang, C.T. / Dickman, M.J. / Essex-Lopresti, A. / Harding, S.V. / Mahadi, N.M. / Marshall, L.E. / Mobbs, G.W. / Mohamed, R. / Nathan, S. / Ngugi, S.A. / Ong, C. / Ooi, W.F. / Partridge, L.J. / Phillips, H.L. / Raih, M.F. / Ruzheinikov, S. / Sarkar-Tyson, M. / Sedelnikova, S.E. / Smither, S.J. / Tan, P. / Titball, R.W. / Wilson, S.A. / Rice, D.W. #1: Journal: To be Published Title: Cloning, purification and crystallographic analysis of a hypothetical protein, BPSL1549, from Burkholderia pseudomallei Authors: Cruz-Migoni, A. / Ruzheinikov, N. / Sedelnikova, E. / Obeng, B. / Chieng, S. / RMohamed, R. / Nathan, S. / Baker, P. / Rice, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tu8.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tu8.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 3tu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tu8_validation.pdf.gz | 417 KB | Display | wwPDB validaton report |
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Full document | 3tu8_full_validation.pdf.gz | 418.3 KB | Display | |
Data in XML | 3tu8_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3tu8_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/3tu8 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/3tu8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23244.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BPSL1549 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63UP7 |
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#2: Chemical | ChemComp-BR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 26% PEG 3350, 0.2M Sodium bromide, 0.1M bis-tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9163 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2008 |
Radiation | Monochromator: Double Crystall Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9163 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→25 Å / Num. all: 103861 / Num. obs: 102823 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.04→1.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.7 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Resolution: 1.04→25 Å / Num. parameters: 19182 / Num. restraintsaints: 24517 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 16 / Occupancy sum hydrogen: 1558.98 / Occupancy sum non hydrogen: 2007.85 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→25 Å
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Refine LS restraints |
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