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Yorodumi- PDB-2ixb: Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ixb | |||||||||
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Title | Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC | |||||||||
Components | ALPHA-N-ACETYLGALACTOSAMINIDASE | |||||||||
Keywords | HYDROLASE / N-ACETYLGALACTOSAMINIDASE / NAD / A-ECO CONVERSION | |||||||||
Function / homology | Function and homology information alpha-N-acetylgalactosaminidase / alpha-N-acetylgalactosaminidase activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | FLAVOBACTERIUM MENINGOSEPTICUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Sulzenbacher, G. / Liu, Q.P. / Bourne, Y. / Henrissat, B. / Clausen, H. | |||||||||
Citation | Journal: Nat.Biotechnol. / Year: 2007 Title: Bacterial Glycosidases for the Production of Universal Red Blood Cells. Authors: Liu, Q.P. / Sulzenbacher, G. / Yuan, H. / Bennett, E.P. / Pietz, G. / Saunders, K. / Spence, J. / Nudelman, E. / Levery, S.B. / White, T. / Neveu, J.M. / Lane, W.S. / Bourne, Y. / Olsson, M. ...Authors: Liu, Q.P. / Sulzenbacher, G. / Yuan, H. / Bennett, E.P. / Pietz, G. / Saunders, K. / Spence, J. / Nudelman, E. / Levery, S.B. / White, T. / Neveu, J.M. / Lane, W.S. / Bourne, Y. / Olsson, M.L. / Henrissat, B. / Clausen, H. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ixb.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ixb.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ixb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ixb_validation.pdf.gz | 768 KB | Display | wwPDB validaton report |
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Full document | 2ixb_full_validation.pdf.gz | 770.1 KB | Display | |
Data in XML | 2ixb_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2ixb_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ixb ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ixb | HTTPS FTP |
-Related structure data
Related structure data | 2ixaSC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 50281.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) FLAVOBACTERIUM MENINGOSEPTICUM (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS References: UniProt: A4Q8F7*PLUS, alpha-N-acetylgalactosaminidase |
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#3: Sugar | ChemComp-A2G / |
-Non-polymers , 4 types, 182 molecules
#2: Chemical | ChemComp-NAD / | ||||
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#4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: 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: 3.44 Å3/Da / Density % sol: 65 % |
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Crystal grow | pH: 6.25 Details: 46-50% 2-METHYL-2,4-PENTANEDIOL (MPD), 75 MM NA-CITRATE PH 6.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 27626 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 43.94 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.4 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IXA Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12.727 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GLOBAL B-FACTORS, CONTAINING RESIDUAL AND TLS COMPONENT HAVE BEEN DEPOSITED.
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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: 40.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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