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Yorodumi- PDB-2w4m: The Crystal Structure of human N-acetylneuraminic acid phosphatas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w4m | ||||||
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Title | The Crystal Structure of human N-acetylneuraminic acid phosphatase, NANP | ||||||
Components | N-ACYLNEURAMINATE-9-PHOSPHATASE | ||||||
Keywords | HYDROLASE / N-ACETYLNEURAMINATE / NEU5AC-9- PHOSPHATE / CARBOHYDRATE METABOLISM / N-ACETYLNEURAMINIC ACID PHOSPHATASE / NANP / HDHD4 / MAGNESIUM / SIALIC ACID | ||||||
Function / homology | Function and homology information N-acylneuraminate-9-phosphatase / N-acetylglucosamine biosynthetic process / N-acylneuraminate-9-phosphatase activity / N-acetylneuraminate biosynthetic process / Sialic acid metabolism / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ugochukwu, E. / Cocking, R. / Yue, W.W. / Pike, A.C.W. / Roos, A. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. ...Ugochukwu, E. / Cocking, R. / Yue, W.W. / Pike, A.C.W. / Roos, A. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of Human N-Acetylneuraminic Acid Phosphatase, Nanp Authors: Ugochukwu, E. / Cocking, R. / Yue, W.W. / Pike, A.C.W. / Roos, A. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w4m.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w4m.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/2w4m ftp://data.pdbj.org/pub/pdb/validation_reports/w4/2w4m | HTTPS FTP |
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-Related structure data
Related structure data | 2gfhS 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
#1: Protein | Mass: 30405.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q8TBE9, N-acylneuraminate-9-phosphatase | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | #4: Chemical | #5: 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: 5.33 Å3/Da / Density % sol: 76.95 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 0.8M NA_PHOSPHATE_(NA_H2_PO4)-4M, 0.16M K_PHOSPHATE_(K2_H_PO4)-4M AT 20 DEGREES C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35.37 Å / Num. obs: 92013 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GFH Resolution: 2.6→35.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 12.328 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / 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: 23.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→35.42 Å
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Refine LS restraints |
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