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Yorodumi- PDB-7an4: MlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7an4 | ||||||
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Title | MlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni complex with GDP-mannose | ||||||
Components | Thymidine diphospho-4-keto-rhamnose 3,5-epimerase | ||||||
Keywords | SUGAR BINDING PROTEIN / epimerise / sugar nucleotide / cupin fold / enzyme | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Naismith, J.H. / Woodward, L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: MghlB with GDP Authors: Naismith, J.H. / Woodward, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7an4.cif.gz | 158 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7an4.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 7an4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7an4_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7an4_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7an4_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 7an4_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/7an4 ftp://data.pdbj.org/pub/pdb/validation_reports/an/7an4 | HTTPS FTP |
-Related structure data
Related structure data | 1dzrS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 21243.232 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) Gene: A0Z41_07375, A4277_09450, B4O43_09685, B7M65_03490, BGG25_09075, BM409_09635, BM444_09010, BM513_08715, BSK70_08235, BSO22_09160, BZL95_08990, C1418_09190, CLC11_09605, CUT57_09155, D6H09_ ...Gene: A0Z41_07375, A4277_09450, B4O43_09685, B7M65_03490, BGG25_09075, BM409_09635, BM444_09010, BM513_08715, BSK70_08235, BSO22_09160, BZL95_08990, C1418_09190, CLC11_09605, CUT57_09155, D6H09_04530, DDO06_09345, DDV78_09325, DMN69_08700, DNA92_09015, DUY83_08160, DYU98_09455, E7P31_08690, E7R39_08745, EID41_09365, F0020_07730, F0E95_08655, F0F84_08705, F0F98_08535, F0G47_08120, F0G48_09050, F0N28_08120, F1N65_08765, F1O83_08575, F6069_09535, F7J52_08685, F7N67_09750, F9736_08800, FJ686_08855, FLI41_08630, FLR61_08490, FM724_09165, FNQ00_09015, FNW64_09490, FQX08_09165, FR479_08460, FVI37_08595, FVM38_08185, FVM79_08160, FVN10_08670, FVY82_08610, FVZ89_08655, FW037_08340, FW114_08530, FW212_08130, FW254_07800, FW615_08225, FW631_08740, FW892_08160, FW922_08210, FWA46_08455, FWB30_08765, FWZ78_00520, FXA21_08555, FXA45_08490, FY829_09115, FZJ28_08750, FZV74_08235, GAU91_08625, GAX51_09520, GCY42_03565, GI147_08930, GI310_08945, GLM94_08700, GPY87_09225, GQ373_08515, GS576_08280, GSX00_06480, GTI33_08365, GTQ72_08215, GV351_09030, GWW43_07680, GXS63_001730, GZD67_001691, VQ12_003125 Production host: Escherichia coli (E. coli) References: UniProt: A0A2U0QM91, UniProt: Q0P8I4*PLUS, dTDP-4-dehydrorhamnose 3,5-epimerase #2: Chemical | ChemComp-GDP / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 31.05 % (w/v) PEG 1500, 0.25 M sodium-potassium phosphate, 3.83 % (v/v) 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Oct 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→56.7 Å / Num. obs: 23972 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.162 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.6→2.67 Å / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1611 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DZR Resolution: 2.6→56.67 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.901 / SU B: 11.204 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.581 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.81 Å2 / Biso mean: 26.456 Å2 / Biso min: 8.03 Å2
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Refinement step | Cycle: final / Resolution: 2.6→56.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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