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Yorodumi- PDB-6oe2: X-Ray Structure of the C-terminal domain (277-440) of Putative ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oe2 | ||||||
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Title | X-Ray Structure of the C-terminal domain (277-440) of Putative chitobiase from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR324A. Re-refinement of 3GGL with correct metal Mn replacing Zn. New metal confirmed with PIXE analysis of original sample. | ||||||
Components | Chitobiase | ||||||
Keywords | HYDROLASE / NESG / BTR324A / Q8A9F0_BACTN / Bacteroides thetaiotaomicron / BT_0865 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Structural Genomics / PIXE | ||||||
Function / homology | Function and homology information protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Snell, E.H. / Garman, E.F. / Lowe, E.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target BtR324A Authors: Kuzin, A. / Neely, H. / Seetharaman, R. / Lee, D. / Ciccosanti, C. / Foote, E.L. / Janjua, H. / Xiao, R. / Nair, R. / Rost, B. / Acton, T. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oe2.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oe2.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 6oe2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oe2_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 6oe2_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 6oe2_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 6oe2_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/6oe2 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/6oe2 | HTTPS FTP |
-Related structure data
Related structure data | 6nlrC 6obyC 3f2zS 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: 18766.789 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 280-440) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: nagJ_1, ERS852430_00185, SAMN02910322_00414 / Details (production host): PET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ MAGIC References: UniProt: A0A173R4M5, UniProt: Q8A9F0*PLUS, protein O-GlcNAcase |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-MN / |
#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: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.75 M magnesium formate, 0.1 M Bis-Tris, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 22, 2009 / Details: MIRRORS |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 4644 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 0 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.484 / Num. unique obs: 0 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F2Z Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 42.275 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.607 Å2
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Refinement step | Cycle: LAST / Resolution: 3→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -30.74 Å / Origin y: -13.65 Å / Origin z: -5.493 Å
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