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Yorodumi- PDB-1xiz: Structural Genomics, The crystal structure of domain IIA of putat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xiz | ||||||
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Title | Structural Genomics, The crystal structure of domain IIA of putative phosphotransferase system specific for mannitol/fructose from Salmonella typhimurium | ||||||
Components | putative phosphotransferase system mannitol/fructose-specific IIA domainPEP group translocation | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / IIA domain / protein structure initiative / Midwest Center for Structural Genomics / MCSG / PSI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Zhang, R. / Joachimiak, G. / Otwinowski, Z. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of domain IIA of putative phosphotransferase system specific for mannitol/fructose from Salmonella typhimurium Authors: Zhang, R. / Joachimiak, G. / Otwinowski, Z. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xiz.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xiz.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/1xiz ftp://data.pdbj.org/pub/pdb/validation_reports/xi/1xiz | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18024.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZL18 #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: 2.1 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.9465 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: May 29, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. all: 37329 / Num. obs: 37292 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.34 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.18 / Num. unique all: 3706 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→33.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 537142.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.0796 Å2 / ksol: 0.350699 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→33.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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