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Yorodumi- PDB-4ipj: Crystal Structure of R314K N-acetyl Neuraminic Acid Synthase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ipj | ||||||
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Title | Crystal Structure of R314K N-acetyl Neuraminic Acid Synthase from Neiserria meningitidis with Malate bound | ||||||
Components | Polysialic acid capsule biosynthesis protein SiaC | ||||||
Keywords | TRANSFERASE / Antifreeze Protein Fold / NANA / N-acetylneuraminic acid / sialic acid / Neisseria meningitidis | ||||||
Function / homology | Function and homology information N-acylneuraminate-9-phosphate synthase activity / glycosylation / carbohydrate biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Joseph, D.D.A. / Jiao, W. / Parker, E.J. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Arg314 Is Essential for Catalysis by N-Acetyl Neuraminic Acid Synthase from Neisseria meningitidis. Authors: Joseph, D.D. / Jiao, W. / Parker, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ipj.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ipj.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ipj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/4ipj ftp://data.pdbj.org/pub/pdb/validation_reports/ip/4ipj | HTTPS FTP |
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-Related structure data
Related structure data | 4ipiC 1xuzS 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: 38495.844 Da / Num. of mol.: 1 / Mutation: R314K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: siaC, NMB0068 / Production host: Escherichia coli (E. coli) References: UniProt: Q7DDU0, UniProt: Q57265*PLUS, N-acetylneuraminate synthase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-LMR / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1.9 M malic acid, 10 mM magnesium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→34.15 Å / Num. all: 19363 / Num. obs: 19363 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 7.3 / Rsym value: 0.405 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XUZ Resolution: 2.15→34.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.403 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 13.706 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→34.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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