[English] 日本語
Yorodumi- PDB-7anc: MlghC, GDP-mannoheptose C4 reductase from Campylobacter jejuni wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7anc | ||||||
---|---|---|---|---|---|---|---|
Title | MlghC, GDP-mannoheptose C4 reductase from Campylobacter jejuni with NADP bound | ||||||
Components | GDP-L-fucose synthase | ||||||
Keywords | SUGAR BINDING PROTEIN / reductase / sugar nucleotide / NADP / enzyme | ||||||
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 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Naismith, J.H. / Woodward, L. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: MghlC Authors: Naismith, J.H. / Woodward, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7anc.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7anc.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 7anc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7anc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7anc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7anc_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 7anc_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/7anc ftp://data.pdbj.org/pub/pdb/validation_reports/an/7anc | HTTPS FTP |
-Related structure data
Related structure data | 1bsvS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39297.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) Gene: fcl, A0Z41_07385, A4277_09460, B4O43_09695, B7M65_03500, BGG25_09085, BM409_09645, BM444_09020, BM513_08725, BSK70_08245, BSO22_09170, C1418_09205, CLC11_09615, CUT57_09340, D6H09_04540, DDV78_ ...Gene: fcl, A0Z41_07385, A4277_09460, B4O43_09695, B7M65_03500, BGG25_09085, BM409_09645, BM444_09020, BM513_08725, BSK70_08245, BSO22_09170, C1418_09205, CLC11_09615, CUT57_09340, D6H09_04540, DDV78_09315, DMN69_08810, DNA92_09025, DYU98_09465, E7P31_08700, E7R39_08755, EID41_09375, F0F26_01770, F0G48_09060, F0N28_08130, F0N82_00455, F1N65_08775, F1O83_08585, F6069_09545, F7N67_09870, F9736_08790, FJ686_08865, FLI41_08640, FM724_09175, FNW64_09505, FVI37_08605, FVM38_08200, FVN10_08680, FVY82_08620, FWZ78_00530, FXA21_08565, FXA45_08500, FY829_09130, FYZ21_00200, FZ860_03225, FZB49_04250, FZJ28_08760, FZL73_00555, GAU91_08635, GAX51_09535, GCY42_03575, GI310_08960, GLM81_05635, GLM94_08710, GPY87_09235, GS576_08295, GTQ72_08225, GV351_09045, GWW43_07690, GXS63_001732, GZD67_001693 Production host: Escherichia coli (E. coli) References: UniProt: A0A2U0QM62, UniProt: Q0P8I6*PLUS, GDP-L-fucose synthase #2: Chemical | #3: 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: 2.75 Å3/Da / Density % sol: 55.31 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 24.63 % (w/v) PEG 8000, 0.1 M Bicine pH 8.5, 0.12 M sodium citrate 0.05 % (w/v). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→66 Å / Num. obs: 94907 / % possible obs: 99.2 % / Redundancy: 3.7 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.66→1.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.76 / Num. unique obs: 7016 / CC1/2: 0.5 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BSV Resolution: 1.66→65.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.229 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.453 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→65.98 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
|