+Open data
-Basic information
Entry | Database: PDB / ID: 1kut | ||||||
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Title | Structural Genomics, Protein TM1243, (SAICAR synthetase) | ||||||
Components | Phosphoribosylaminoimidazole-succinocarboxamide synthase | ||||||
Keywords | STRUCTURAL GENOMICS / LIGASE / SAICAR synthetase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Zhang, R. / Skarina, T. / Beasley, S. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer. Authors: Zhang, R. / Skarina, T. / Evdokimova, E. / Edwards, A. / Savchenko, A. / Laskowski, R. / Cuff, M.E. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kut.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kut.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kut_validation.pdf.gz | 412.5 KB | Display | wwPDB validaton report |
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Full document | 1kut_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | 1kut_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1kut_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/1kut ftp://data.pdbj.org/pub/pdb/validation_reports/ku/1kut | 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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Unit cell |
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Details | Protein TM86 existed in dimer. Chain A and Chain B represent two molecules in the dimer |
-Components
#1: Protein | Mass: 26508.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1243 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9X0X0, phosphoribosylaminoimidazolesuccinocarboxamide synthase #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: 2.07 Å3/Da / Density % sol: 40.49 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,0.9791,0.95200 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Sep 10, 2001 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.14→50 Å / Num. all: 23684 / Num. obs: 23637 / % possible obs: 99.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.28 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 20.6 | ||||||||||||
Reflection shell | Resolution: 2.14→2.25 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.74 / Num. unique all: 3378 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 316887.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: hlml refinement target of CNS was used in the refinement. The number of reflections used in refinement include Friedel pairs. Therefore, the number of reflections for refinement is larger ...Details: hlml refinement target of CNS was used in the refinement. The number of reflections used in refinement include Friedel pairs. Therefore, the number of reflections for refinement is larger than the number collected.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.8597 Å2 / ksol: 0.497007 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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