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Yorodumi- PDB-1tzf: X-ray Crystal Structure of alpha-D-glucose-1-phosphate cytidylylt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tzf | ||||||
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Title | X-ray Crystal Structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi | ||||||
Components | Glucose-1-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / nucleotidyltransferase / mixed alpha/beta fold | ||||||
Function / homology | Function and homology information glucose-1-phosphate cytidylyltransferase / glucose-1-phosphate cytidylyltransferase activity / O antigen biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Koropatkin, N.M. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi Authors: Koropatkin, N.M. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tzf.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tzf.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tzf_validation.pdf.gz | 803.9 KB | Display | wwPDB validaton report |
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Full document | 1tzf_full_validation.pdf.gz | 814.1 KB | Display | |
Data in XML | 1tzf_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1tzf_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tzf ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tzf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is a hexamer, generated from the monomer in the asymmetric unit by the operations: ROTATION MATRIX: -0.50000 -0.86603 0.00000 0.86603 -0.50000 0.00001 -0.00001 0.00000 1.00000 TRANSLATION VECTOR IN AS 0.00043 0.00017 0.00008 ROTATION MATRIX: -0.50000 0.86602 0.00000 -0.86602 -0.50000 0.00000 0.00000 0.00000 1.00000 TRANSLATION VECTOR IN AS 0.00046 0.00027 0.00009 ROTATION MATRIX: -1.00000 0.00000 0.00000 0.00000 1.00000 0.00001 0.00000 0.00001 -1.00000 TRANSLATION VECTOR IN AS 0.00020 -0.00001 81.14987 ROTATION MATRIX: 0.50000 0.86602 0.00000 0.86602 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS 0.00082 0.00015 81.15000 ROTATION MATRIX: 0.50000 -0.86603 0.00000 -0.86603 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS 0.00045 0.00058 81.14999 These are the rotation and translation operations to be performed on the original monomer to generate the next five subunits of the complete hexamer 'P 63 2 2' 1 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 'P 63 2 2' 3 0 -1 0 1 -1 0 0 0 1 0 0 0 0 0 0 'P 63 2 2' 5 -1 1 0 -1 0 0 0 0 1 0 0 0 0 0 0 'P 63 2 2' 7 1 -1 0 0 -1 0 0 0 -1 0 0 0 0 0 0 'P 63 2 2' 9 -1 0 0 -1 1 0 0 0 -1 0 0 0 0 0 0 'P 63 2 2' 11 0 1 0 1 0 0 0 0 -1 0 0 0 0 0 0 'P 63 2 2' 2 1 -1 0 1 0 0 0 0 1 0 0 0 0 1 2 'P 63 2 2' 4 -1 0 0 0 -1 0 0 0 1 0 0 0 0 1 2 'P 63 2 2' 6 0 1 0 -1 1 0 0 0 1 0 0 0 0 1 2 'P 63 2 2' 8 0 -1 0 -1 0 0 0 0 -1 0 0 0 0 1 2 'P 63 2 2' 10 -1 1 0 0 1 0 0 0 -1 0 0 0 0 1 2 'P 63 2 2' 12 1 0 0 1 -1 0 0 0 -1 0 0 0 0 1 2 |
-Components
#1: Protein | Mass: 29203.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: complexed with cytidyl-5'-phosphate-glucosyl-6-phosphate Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria) Species: Salmonella enterica / Strain: CT18 / Gene: rfbF / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS References: UniProt: P26396, UniProt: Q8Z5I4*PLUS, glucose-1-phosphate cytidylyltransferase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-C5G / [ |
#4: 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: 3 Å3/Da / Density % sol: 58.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, Ammonium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9641 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 29, 2004 |
Radiation | Monochromator: Double crystal Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9641 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 22401 / Num. obs: 22358 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rsym value: 0.067 / Net I/σ(I): 65.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 9.9 / Num. unique all: 2163 / Rsym value: 0.176 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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