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Yorodumi- PDB-2yi1: Crystal structure of N-Acetylmannosamine kinase in complex with N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yi1 | ||||||
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Title | Crystal structure of N-Acetylmannosamine kinase in complex with N- acetyl mannosamine 6-phosphate and ADP. | ||||||
Components | BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE | ||||||
Keywords | TRANSFERASE / SUGAR KINASE / ROK FAMILY | ||||||
Function / homology | Function and homology information Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism ...Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism / hydrolase activity, hydrolyzing O-glycosyl compounds / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Martinez, J. / Nguyen, L.D. / Tauberger, E. / Hinderlich, S. / Reutter, W. / Fan, H. / Saenger, W. / Moniot, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition Authors: Martinez, J. / Nguyen, L.D. / Tauberger, E. / Hinderlich, S. / Reutter, W. / Fan, H. / Saenger, W. / Moniot, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yi1.cif.gz | 142.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yi1.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yi1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2yi1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2yi1_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2yi1_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/2yi1 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/2yi1 | HTTPS FTP |
-Related structure data
Related structure data | 2yhwSC 2yhyC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36639.016 Da / Num. of mol.: 1 Fragment: N-ACETYLMANNOSAMINE KINASE DOMAIN, RESIDUES 406-720 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A-MNK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9Y223, N-acylmannosamine kinase |
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-Sugars , 2 types, 2 molecules
#2: Sugar | ChemComp-BMX / |
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#3: Sugar | ChemComp-BM3 / |
-Non-polymers , 9 types, 155 molecules
#4: Chemical | ChemComp-MG / | ||||||||||||||
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#5: Chemical | #6: Chemical | ChemComp-2PE / | #7: Chemical | ChemComp-PG4 / | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-ACT / | #10: Chemical | ChemComp-ADP / | #11: Chemical | ChemComp-ZN / | #12: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | 2-(ACETYLAMINO)-6-(PHOSPHATE)-2-DEOXY-ALPHA-D-MANNOPYRANOSE (BMX): N ACETYL MANNOSAMINE ...2-(ACETYLAMIN |
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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: 2.85 Å3/Da / Density % sol: 56.82 % / Description: NONE |
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Crystal grow | Details: 0.2 M CALCIUM ACETATE, 0.1M SODIUM CACODYLATE PH 6.5 AND 40% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.4 Å / Num. obs: 24925 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YHW Resolution: 2.15→41.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.828 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.143 / 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: 37.126 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→41.4 Å
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Refine LS restraints |
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