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Yorodumi- PDB-2qgi: The UDP complex structure of the sixth gene product of the F1-ATP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qgi | ||||||
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Title | The UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus | ||||||
Components | ATP synthase subunits region ORF 6 | ||||||
Keywords | TRANSFERASE / MAJASTRIDIN / ATPASE OPERON / GLYCOSYL TRANSFERASE / ROSSMANN FOLD / UDP-COMPLEX | ||||||
Function / homology | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / : / URIDINE-5'-DIPHOSPHATE / ATP synthase subunits region ORF 6 Function and homology information | ||||||
Biological species | Rhodobacter blasticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Enroth, C. / Strid, A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2008 Title: Crystal structure of a protein, structurally related to glycosyltransferases, encoded in the Rhodobacter blasticus atp operon. Authors: Enroth, C. / Strid, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qgi.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qgi.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/2qgi ftp://data.pdbj.org/pub/pdb/validation_reports/qg/2qgi | HTTPS FTP |
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-Related structure data
Related structure data | 2nxvSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The assymmetric unit contains one biological unit, i.e. a dimer. |
-Components
#1: Protein | Mass: 28720.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter blasticus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P05449 #2: Chemical | #3: Chemical | ChemComp-UDP / | #4: 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: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM sodium citrate (pH6.0) and 75mM magnesium acetate. Mixed 4+4ul with protein sample, hanging drop, vapor diffusion, temperature 298K., VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.043 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 93646 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.071 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 13554 / Rsym value: 0.388 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2NXV Resolution: 1.65→12.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.352 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.201 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→12.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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