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Yorodumi- PDB-3hz7: Crystal Structure of the SirA-like protein (DSY4693) from Desulfi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hz7 | ||||||
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Title | Crystal Structure of the SirA-like protein (DSY4693) from Desulfitobacterium hafniense, Northeast Structural Genomics Consortium Target DhR2A | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information Selenium metabolism protein YedF / TusA-like domain / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / DsrEFH-like / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Desulfitobacterium hafniense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target DhR2A Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / 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 | 3hz7.cif.gz | 24.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hz7.ent.gz | 17.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hz7 ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hz7 | 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: 9551.410 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-79 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense (bacteria) Strain: Y51 / Gene: DSY4693 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q24NB0 |
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#2: Chemical | ChemComp-SX / |
#3: Water | ChemComp-HOH / |
Sequence details | THE CURRENT CRYSTAL STRUCTURE SUGGESTS THAT THERE IS AN ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.47 % |
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Crystal grow | Temperature: 277 K / pH: 7 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 100mM Bis-Tris Propane (pH 7), 40% PEG4k, and 100mM calcium chloride, 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: 0.97976 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97976 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 11596 / Num. obs: 11492 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.033 / Net I/σ(I): 62.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 10 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 10.1 / Num. unique all: 1159 / Rsym value: 0.201 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.98 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 504513.781 / 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: 55.676 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
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