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Yorodumi- PDB-3hxl: Crystal Structure of the sheath tail protein (DSY3957) from Desul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hxl | ||||||
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Title | Crystal Structure of the sheath tail protein (DSY3957) from Desulfitobacterium hafniense, Northeast Structural Genomics Consortium Target DhR18 | ||||||
Components | uncharacterized protein DSY3957 | ||||||
Keywords | structural genomics / unknown function / alpha-beta three-domained protein. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information Ribosomal Protein S8; Chain: A, domain 1 - #220 / Dna Ligase; domain 1 - #360 / Dihydrodipicolinate Reductase; domain 2 - #90 / Rossmann fold - #11790 / Immunoglobulin-like - #4290 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain ...Ribosomal Protein S8; Chain: A, domain 1 - #220 / Dna Ligase; domain 1 - #360 / Dihydrodipicolinate Reductase; domain 2 - #90 / Rossmann fold - #11790 / Immunoglobulin-like - #4290 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Ribosomal Protein S8; Chain: A, domain 1 / Dihydrodipicolinate Reductase; domain 2 / Dna Ligase; domain 1 / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Desulfitobacterium hafniense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target DhR18 Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, 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 | 3hxl.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hxl.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/3hxl ftp://data.pdbj.org/pub/pdb/validation_reports/hx/3hxl | 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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Details | The present crystal structure is mostly monomer. However, this protein oligomerizes when several hundred copies of it form the sheath tail of the phage. |
-Components
#1: Protein | Mass: 48565.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense (bacteria) Strain: Y51 / Gene: DSY3957 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q24QE6 |
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#2: 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: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 277 K / Method: microbatch, under oil / pH: 7.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 100 mM Tris-HCl (pH 7.5), 10% PEG3350, and 20% ethylene glycol., microbatch, under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 82241 / Num. obs: 80185 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.036 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.4 / Num. unique all: 8130 / Rsym value: 0.169 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 359617.625 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.528 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
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