+Open data
-Basic information
Entry | Database: PDB / ID: 1qg8 | ||||||
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Title | NATIVE (MAGNESIUM-CONTAINING) SPSA FROM BACILLUS SUBTILIS | ||||||
Components | PROTEIN (SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA) | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE | ||||||
Function / homology | Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / 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 / Spore coat polysaccharide biosynthesis protein SpsA Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å | ||||||
Authors | Charnock, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms. Authors: Charnock, S.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qg8.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qg8.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qg8_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 1qg8_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 1qg8_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1qg8_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qg8 ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qg8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30090.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GLYCEROL MAGNESIUM / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SPSA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: P39621 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 2.04 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: 15% PEG 8000, 100MM HEPES BUFFER PH 8.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 39 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Charnock, S.J., (1999) Acta Crystallogr., D55, 677. | ||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC / Detector: CCD / Date: Jun 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25.8 Å / Num. obs: 43230 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.27 / % possible all: 86 |
Reflection shell | *PLUS % possible obs: 88 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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