[English] 日本語
Yorodumi- PDB-7m13: Crystal structure of CJ1428, a GDP-D-GLYCERO-L-GLUCO-HEPTOSE SYNT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m13 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of CJ1428, a GDP-D-GLYCERO-L-GLUCO-HEPTOSE SYNTHASE from campylobacter jejuni in the presence of NADPH | |||||||||
Components | GDP-L-fucose synthase | |||||||||
Keywords | OXIDOREDUCTASE / gluco-heptose synthase / capsular polysaccharide | |||||||||
Function / homology | Function and homology information GDP-L-fucose synthase / GDP-L-fucose synthase activity / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity Similarity search - Function | |||||||||
Biological species | Campylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Anderson, T.K. / Thoden, J.B. / Raushel, F.M. / Holden, H.M. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Biosynthesis of d- glycero -l- gluco -Heptose in the Capsular Polysaccharides of Campylobacter jejuni . Authors: Huddleston, J.P. / Anderson, T.K. / Girardi, N.M. / Thoden, J.B. / Taylor, Z. / Holden, H.M. / Raushel, F.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7m13.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7m13.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 7m13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m13_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7m13_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7m13_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 7m13_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/7m13 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/7m13 | HTTPS FTP |
-Related structure data
Related structure data | 7m14C 7m15C 1fxsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39791.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter) Strain: ATCC 700819 / NCTC 11168 / Gene: fcl, Cj1428c / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P8I6, GDP-L-fucose synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 16-20% PEG-5000, 150 mM MgCL2, 100 mM MOPS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9878 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9878 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 129208 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.069 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 6167 / Rsym value: 0.253 / % possible all: 92.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1fxs Resolution: 1.5→30.95 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.105 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.78 Å2 / Biso mean: 22.485 Å2 / Biso min: 6.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→30.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|