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Yorodumi- PDB-4ag9: C. elegans glucosamine-6-phosphate N-acetyltransferase (GNA1): te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ag9 | ||||||
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Title | C. elegans glucosamine-6-phosphate N-acetyltransferase (GNA1): ternary complex with coenzyme A and GlcNAc | ||||||
Components | GLUCOSAMINE-6-PHOSPHATE N-ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / monosaccharide binding / endoplasmic reticulum-Golgi intermediate compartment / Golgi apparatus / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | CAENORHABDITIS ELEGANS (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Dorfmueller, H.C. / Fang, W. / Rao, F.V. / Blair, D.E. / Attrill, H. / Shepherd, S.M. / van Aalten, D.M.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structural and Biochemical Characterization of a Trapped Coenzyme a Adduct of Caenorhabditis Elegans Glucosamine-6-Phosphate N-Acetyltransferase 1. Authors: Dorfmueller, H.C. / Fang, W. / Rao, F.V. / Blair, D.E. / Attrill, H. / Van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ag9.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ag9.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ag9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ag9_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4ag9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4ag9_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 4ag9_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/4ag9 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/4ag9 | HTTPS FTP |
-Related structure data
Related structure data | 4ag7SC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 18481.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUE CYS141 FORMS A DISULPHIDE WITH THE COA. CYS158 FROM THE A AND B CHAINS FORM A DISULPHIDE Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Strain: COSMID B0024 Description: C. ELEGANS COSMID B0024 DNA (SANGER INSTITUTE, CAMBRIDGESHIRE) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: Q17427, glucosamine-phosphate N-acetyltransferase #2: Chemical | #3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Details: 5 MM ACCOA, GLCN-6-P, GLCNAC AND 0.1 M TRIS-HYDROCHLORIDE PH 8.5, 0.2 M SODIUM ACETATE TRIHYDRATE AND 30% (V/V) PEG 3350 AND 11 MM BACL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 34633 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.5 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AG7 Resolution: 1.76→14.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.692 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.121 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→14.99 Å
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Refine LS restraints |
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